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Ni T, Zhao RH, Wu JF, Li CY, Xue G, Lin X. KLK7, KLK10, and KLK11 in Papillary Thyroid Cancer: Bioinformatic Analysis and Experimental Validation. Biochem Genet 2024:10.1007/s10528-024-10679-8. [PMID: 38316654 DOI: 10.1007/s10528-024-10679-8] [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: 05/30/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024]
Abstract
Despite many studies on papillary thyroid carcinoma (PTC) in the past few decades, some critical and significant genes remain undiscovered. To explore genes that may play crucial roles in PTC, a detailed analysis of the expression levels, mutations, and clinical significance of Kallikrein-related peptidases (KLKs) family genes in PTC was undertaken to provide new targets for the precise treatment of the disease. A comprehensive analysis of KLK family genes was performed using various online tools, such as GEPIA, Kaplan-Meier Plotter, LinkedOmics, GSCA, TIMER, and Cluego. KLK7, KLK10, and KLK11 were critical factors of KLK family genes. Then, functional assays were carried out on KLK7/10/11 to determine their proliferation, migration, and invasion capabilities in PTC. The mRNA expression levels of KLK7, KLK10, KLK11, and KLK13 were significantly elevated in thyroid carcinoma, while KLK1, KLK2, KLK3 and KLK4 mRNA levels were decreased compared to normal tissues. Correlations between KLK2/7-12/15 expression levels and tumor stage were also observed in thyroid carcinoma. Survival analysis demonstrated that KLK4/5/7/9-12/14 was associated with overall survival in patients with thyroid cancer. Not only were KLK genes strongly associated with cancer-related pathways, but also KLK7/10/11 was associated with immune-cell infiltration. Finally, silencing KLK7/10/11 impaired human papillary thyroid carcinoma cells' growth, migration ability, and invasiveness. The increased expression of KLK7, KLK10, and KLK11 may serve as molecular markers to identify PTC patients. KLK7, KLK10, and KLK11 could be potential prognostic indicators and targets for precision therapy against PTC.
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Affiliation(s)
- Tao Ni
- Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, 075000, China
| | - Ru-Hua Zhao
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou, 075000, China
| | - Jing-Fang Wu
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou, 075000, China
| | - Chao-You Li
- Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, 075000, China
| | - Gang Xue
- Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, 075000, China.
| | - Xu Lin
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou, 075000, China.
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Liu S, Wang J, Chen S, Han Z, Wu H, Chen H, Duan Y. C/EBPβ Coupled with E2F2 Promoted the Proliferation of hESC-Derived Hepatocytes through Direct Binding to the Promoter Regions of Cell-Cycle-Related Genes. Cells 2023; 12:cells12030497. [PMID: 36766839 PMCID: PMC9914899 DOI: 10.3390/cells12030497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/09/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Human embryonic stem cells (hESCs) hold the potential to solve the problem of the shortage of functional hepatocytes in clinical applications and drug development. However, a large number of usable hepatocytes derived from hESCs cannot be effectively obtained due to the limited proliferation capacity. In this study, we found that enhancement of liver transcription factor C/EBPβ during hepatic differentiation could not only significantly promote the expression of hepatic genes, such as albumin, alpha fetoprotein, and alpha-1 antitrypsin, but also dramatically reinforce proliferation-related phenotypes, including increasing the expression of proliferative genes, such as CDC25C, CDC45L, and PCNA, and the activation of cell cycle and DNA replication pathways. In addition, the analysis of CUT&Tag sequencing further revealed that C/EBPβ is directly bound to the promoter region of proliferating genes to promote cell proliferation; this interaction between C/EBPβ and DNA sequences of the promoters was verified by luciferase assay. On the contrary, the knockdown of C/EBPβ could significantly inhibit the expression of the aforementioned proliferative genes. RNA transcriptome analysis and GSEA enrichment indicated that the E2F family was enriched, and the expression of E2F2 was changed with the overexpression or knockdown of C/EBPβ. Moreover, the results of CUT&Tag sequencing showed that C/EBPβ also directly bound the promoter of E2F2, regulating E2F2 expression. Interestingly, Co-IP analysis exhibited a direct binding between C/EBPβ and E2F2 proteins, and this interaction between these two proteins was also verified in the LO2 cell line, a hepatic progenitor cell line. Thus, our results demonstrated that C/EBPβ first initiated E2F2 expression and then coupled with E2F2 to regulate the expression of proliferative genes in hepatocytes during the differentiation of hESCs. Therefore, our findings open a new avenue to provide an in vitro efficient approach to generate proliferative hepatocytes to potentially meet the demands for use in cell-based therapeutics as well as for pharmaceutical and toxicological studies.
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Affiliation(s)
- Shoupei Liu
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Jue Wang
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Sen Chen
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Zonglin Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Haibin Wu
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Honglin Chen
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Correspondence: (H.C.); (Y.D.)
| | - Yuyou Duan
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Correspondence: (H.C.); (Y.D.)
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[Overexpression of CLEC5A inhibits cell proliferation and metastasis and reverses epithelial-mesenchymal transition in hepatocellular carcinoma]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2023; 43:85-91. [PMID: 36856214 DOI: 10.12122/j.issn.1673-4254.2023.01.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
OBJECTIVE To evaluate the effects of CLEC5A expression level on cell proliferation, migration and invasion and epithelial-mesenchymal transition (EMT) in hepatocellular carcinoma (HCC) and explore the role of CLEC5A in the tumorigenesis and progression of HCC. METHODS The expression level of CLEC5A was detected in 50 pairs of HCC and adjacent tissues using immunohistochemical staining, and its association with clinicopathological parameters of HCC patients was analyzed. Cultured HCC cell line SK-HEP-1 was transfected with a lentiviral vector overexpressing CLEC5A, and the transfection efficiency was verified using real-time fluorescence quantitative PCR and Western blotting. The changes in proliferation, migration and invasion abilities of the transfected cells were analyzed using CCK-8, 5-ethynyl-29-deoxyuridine (EdU) and Transwell assays, and EMT of the cells was determined using Western blotting. RESULTS The protein expression level of CLEC5A was significantly lower in HCC tissues than in the adjacent tissues (P < 0.001). The expression level of CLEC5A was significantly correlated with tumor size (P=0.008), tumor number (P=0.010), histological differentiation (P=0.016), microvascular invasion (P=0.024) and BCLC stage (P=0.040). In SK-HEP-1 cells, overexpression of CLEC5A obviously inhibited the cell proliferation, migration and invasion and reversed EMT phenotype of the cells. CONCLUSION CLEC5A is a potential HCC suppressor gene and may serve as a promising therapeutic target for HCC.
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Wang Z, Pang J, Wang L, Dong Q, Jin D. CEBPB regulates the bile acid receptor FXR to accelerate colon cancer progression by modulating aerobic glycolysis. J Clin Lab Anal 2022; 36:e24703. [PMID: 36129029 DOI: 10.1002/jcla.24703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/24/2022] [Accepted: 09/04/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Aerobic glycolysis is a main characteristic of tumors, and inhibited glycolysis impedes the tumor development. Farnesoid X Receptor (FXR) mainly regulates bile acid metabolism. In this research, we mainly investigated whether FXR was involved in the regulation of glycolysis in colon cancer. METHODS The differential expression analysis was performed on FXR and Enhancer Binding Protein Beta (CEBPB) data in colon cancer downloaded from The Cancer Genome Atlas (TCGA) database. Western blot and qRT-PCR were used to detect the expression levels of CEBPB and FXR. The upstream gene of FXR was predicted through bioinformatic analysis. ChIP and dual luciferease assays were performed to confirm the targeted relationship between CEBPB and FXR. Gene Set Enrichment Analysis (GSEA) was performed on FXR. Finally, the glycolysis capabilities of cells in each treatment group were detected. CCK-8, colony formation assay and flow cytometry were performed to test proliferation and apoptosis of colon cancer cells. RESULTS FXR was lowly expressed at the cell level in colon cancer. In vitro assays verified the antitumor effect of FXR on colon cancer. ChIP and dual luciferase assays verified that transcription factor CEBPB bound with the promotor region of FXR, and negatively regulated the expression of FXR. Cell function assays proved that silenced expression of FXR promoted glycolysis, which promoted the development of colon cancer cells. CONCLUSION The study on FXR-regulated glycolysis of colon cancer cells helps us to further understand the molecular mechanism by which FXR regulated the development of colon cancer cells.
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Affiliation(s)
- Zhengrong Wang
- Department of Oncology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China.,Department of Oncology, Enze Hospital, Taizhou Enze Medical Center (Group), Taizhou, China
| | - Jinghuan Pang
- Department of Functional Examination, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China
| | - Lingyan Wang
- Department of Oncology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China
| | - Qinhui Dong
- Department of Oncology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China
| | - Dan Jin
- Department of Oncology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China
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Nowak JK, Adams AT, Kalla R, Lindstrøm JC, Vatn S, Bergemalm D, Keita ÅV, Gomollón F, Jahnsen J, Vatn MH, Ricanek P, Ostrowski J, Walkowiak J, Halfvarson J, Satsangi J. Characterisation of the Circulating Transcriptomic Landscape in Inflammatory Bowel Disease Provides Evidence for Dysregulation of Multiple Transcription Factors Including NFE2, SPI1, CEBPB, and IRF2. J Crohns Colitis 2022; 16:1255-1268. [PMID: 35212366 PMCID: PMC9426667 DOI: 10.1093/ecco-jcc/jjac033] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/11/2022] [Accepted: 02/23/2022] [Indexed: 01/11/2023]
Abstract
AIM To assess the pathobiological and translational importance of whole-blood transcriptomic analysis in inflammatory bowel disease [IBD]. METHODS We analysed whole-blood expression profiles from paired-end sequencing in a discovery cohort of 590 Europeans recruited across six countries in the IBD Character initiative (newly diagnosed patients with Crohn's disease [CD; n = 156], ulcerative colitis [UC; n = 167], and controls [n = 267]), exploring differential expression [DESeq2], co-expression networks [WGCNA], and transcription factor involvement [EPEE, ChEA, DoRothEA]. Findings were validated by analysis of an independent replication cohort [99 CD, 100 UC, 95 controls]. In the discovery cohort, we also defined baseline expression correlates of future treatment escalation using cross-validated elastic-net and random forest modelling, along with a pragmatic ratio detection procedure. RESULTS Disease-specific transcriptomes were defined in IBD [8697 transcripts], CD [7152], and UC [8521], with the most highly significant changes in single genes, including CD177 (log2-fold change [LFC] = 4.63, p = 4.05 × 10-118), MCEMP1 [LFC = 2.45, p = 7.37 × 10-109], and S100A12 [LFC = 2.31, p = 2.15 × 10-93]. Significantly over-represented pathways included IL-1 [p = 1.58 × 10-11], IL-4, and IL-13 [p = 8.96 × 10-9]. Highly concordant results were obtained using multiple regulatory activity inference tools applied to the discovery and replication cohorts. These analyses demonstrated central roles in IBD for the transcription factors NFE2, SPI1 [PU.1], CEBPB, and IRF2, all regulators of cytokine signalling, based on a consistent signal across cohorts and transcription factor ranking methods. A number of simple transcriptome-based models were associated with the need for treatment escalation, including the binary CLEC5A/CDH2 expression ratio in UC (hazard ratio = 23.4, 95% confidence interval [CI] 5.3-102.0). CONCLUSIONS Transcriptomic analysis has allowed for a detailed characterisation of IBD pathobiology, with important potential translational implications.
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Affiliation(s)
- Jan K Nowak
- Corresponding authors: Dr Jan K. Nowak, Translational Gastroenterology Unit, Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford OX3 9DU, UK.
| | | | - Rahul Kalla
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jonas C Lindstrøm
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Simen Vatn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Åsa V Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | - Jørgen Jahnsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- EpiGen Institute, Akershus University Hospital, University of Oslo, Oslo, Norway
| | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Jerzy Ostrowski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Jaroslaw Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Jack Satsangi
- Jack Satsangi, Translational Gastroenterology Unit, Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK.
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Chen R, Wu W, Chen SY, Liu ZZ, Wen ZP, Yu J, Zhang LB, Liu Z, Zhang J, Luo P, Zeng WJ, Cheng Q. A Pan-Cancer Analysis Reveals CLEC5A as a Biomarker for Cancer Immunity and Prognosis. Front Immunol 2022; 13:831542. [PMID: 35979347 PMCID: PMC9376251 DOI: 10.3389/fimmu.2022.831542] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
Background CLEC5A is a member of the C-type lectin superfamily. It can activate macrophages and lead to a series of immune-inflammation reactions. Previous studies reveal the role of CLEC5A in infection and inflammation diseases. Method We acquire and analyze data from The Cancer Genome Atlas (TCGA) database, Genotype-Tissue Expression (GTEx) database, and other comprehensive databases via GSCALite, cBioPortal, and TIMER 2.0 platforms or software. Single-cell sequencing analysis was performed for quantifying the tumor microenvironment of several types of cancers. Results CLEC5A is differentially expressed in a few cancer types, of which overexpression accompanies low overall survival of patients. DNA methylation mainly negatively correlates with CLEC5A expression. Moreover, CLEC5A is positively related to immune infiltration, including macrophages, cancer-associated fibroblasts (CAFs), and regulatory T cells (Tregs). Immune checkpoint genes are significantly associated with CLEC5A expression in diverse cancers. In addition, CLEC5A expression correlates with mismatch repair (MMR) in several cancers. Tumor mutation burden (TMB), microsatellite instability (MSI), and neoantigens show a positive association with CLEC5A expression in several cancers. Furthermore, CLEC5A in cancer correlates with signal transduction, the immune system, EMT, and apoptosis process. The drug sensitivity analysis screens out potential therapeutic agents associated with CLEC5A expression, including FR-180204, Tivozanib, OSI-930, Linifanib, AC220, VNLG/124, Bexarotene, omacetaxine mepesuccinate, narciclasine, leptomycin B, PHA-793887, LRRK2-IN-1, and CR-1-31B. Conclusion CLEC5A overexpresses in multiple cancers in contrast to normal tissues, and high CLEC5A expression predicts poor prognosis of patients and immune infiltration. CLEC5A is a potential prognostic biomarker of diverse cancers and a target for anti-tumor therapy.
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Affiliation(s)
- Rui Chen
- Department of Neurosurgery, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Wantao Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Si-Yu Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zheng-Zheng Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhi-Peng Wen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Yu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Pharmacy, The Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, China
| | - Long-Bo Zhang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Neurosurgery, and Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT, United States
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wen-Jing Zeng
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Quan Cheng, ; Wen-Jing Zeng,
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Quan Cheng, ; Wen-Jing Zeng,
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Hassan M, Yasir M, Shahzadi S, Kloczkowski A. Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies. ACS OMEGA 2022; 7:19243-19260. [PMID: 35721972 PMCID: PMC9202290 DOI: 10.1021/acsomega.2c00518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/12/2022] [Indexed: 05/14/2023]
Abstract
Novel drug development is a time-consuming process with relatively high debilitating costs. To overcome this problem, computational drug repositioning approaches are being used to predict the possible therapeutic scaffolds against different diseases. In the current study, computational drug repositioning approaches were employed to fetch the promising drugs from the pool of FDA-approved drugs against Ewing sarcoma. The binding interaction patterns and conformational behaviors of screened drugs within the active region of Ewing sarcoma protein (EWS) were confirmed through molecular docking profiles. Furthermore, pharmacogenomics analysis was employed to check the possible associations of selected drugs with Ewing sarcoma genes. Moreover, the stability behavior of selected docked complexes (drugs-EWS) was checked by molecular dynamics simulations. Taken together, astemizole, sulfinpyrazone, and pranlukast exhibited a result comparable to pazopanib and can be used as a possible therapeutic agent in the treatment of Ewing sarcoma.
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Affiliation(s)
- Mubashir Hassan
- Institute
of Molecular Biology and Biotechnology, The University of Lahore, Defense Road Campus, Lahore 54590, Pakistan
- The
Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio 43205, United States
- ,
| | - Muhammad Yasir
- Institute
of Molecular Biology and Biotechnology, The University of Lahore, Defense Road Campus, Lahore 54590, Pakistan
| | - Saba Shahzadi
- Institute
of Molecular Sciences and Bioinformatics (IMSB), Nisbet Road, Lahore 52254, Pakistan
| | - Andrzej Kloczkowski
- The
Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio 43205, United States
- Department
of Pediatrics, The Ohio State University, Columbus, Ohio 43205, United States
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Rong L, Chen B, Liu K, Liu B, He X, Liu J, Li J, He M, Zhu L, Liu K, Shi X, Shuai Y, Jin L. CircZDBF2 up-regulates RNF145 by ceRNA model and recruits CEBPB to accelerate oral squamous cell carcinoma progression via NFκB signaling pathway. J Transl Med 2022; 20:148. [PMID: 35365168 PMCID: PMC8973790 DOI: 10.1186/s12967-022-03347-1] [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: 11/26/2021] [Accepted: 03/10/2022] [Indexed: 11/26/2022] Open
Abstract
Background Oral squamous cell carcinoma (OSCC), as one of the commonest malignancies showing poor prognosis, has been increasingly suggested to be modulated by circular RNAs (circRNAs). Through GEO (Gene Expression Omnibus) database, a circRNA derived from ZDBF2 (circZDBF2) was uncovered to be with high expression in OSCC tissues, while how it may function in OSCC remains unclear. Methods CircZDBF2 expression was firstly verified in OSCC cells via qRT-PCR. CCK-8, along with colony formation, wound healing, transwell and western blot assays was performed to assess the malignant cell behaviors in OSCC cells. Further, RNA pull down assay, RIP assay, as well as luciferase reporter assay was performed to testify the interaction between circZDBF2 and RNAs. Results CircZDBF2 expressed at a high level in OSCC cells and it accelerated OSCC cell proliferation, migration, invasion as well as EMT (epithelial-mesenchymal transition) process. Further, circZDBF2 sponged miR-362-5p and miR-500b-5p in OSCC cells to release their target ring finger protein 145 (RNF145). RNF145 expressed at a high level in OSCC cells and circZDBF2 facilitated RNF145 transcription by recruiting the transcription factor CCAAT enhancer binding protein beta (CEBPB). Moreover, RNF145 activated NFκB (nuclear factor kappa B) signaling pathway and regulated IL-8 (C-X-C motif chemokine ligand 8) transcription. Conclusion CircZDBF2 up-regulated RNF145 expression by sponging miR-362-5p and miR-500b-5p and recruiting CEBPB, thereby promoting OSCC progression via NFκB signaling pathway. The findings recommend circZDBF2 as a probable therapeutic target for OSCC. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03347-1.
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Affiliation(s)
- Liang Rong
- Department of Stomatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Bo Chen
- Department of Stomatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Ke Liu
- Department of Stomatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Bingyao Liu
- Department of Stomatology, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, Jiangsu, China
| | - Xinyao He
- Department of Stomatology, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, Jiangsu, China.,Department of Endodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210002, Jiangsu, China
| | - Juan Liu
- Department of Stomatology, Jinling Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Junxia Li
- Department of Stomatology, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, Jiangsu, China
| | - Maodian He
- Department of Stomatology, Jinling Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Lei Zhu
- Department of Stomatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Ke Liu
- Department of Stomatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Xiaolei Shi
- Department of Stomatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Yi Shuai
- Department of Stomatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China.
| | - Lei Jin
- Department of Stomatology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, Jiangsu, China.
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Fu Y, He G, Liu Z, Wang J, Zhang Z, Bao Q, Wen J, Jin Z, Zhang W. Exploration and Validation of a Novel Inflammatory Response-Associated Gene Signature to Predict Osteosarcoma Prognosis and Immune Infiltration. J Inflamm Res 2021; 14:6719-6734. [PMID: 34916821 PMCID: PMC8668229 DOI: 10.2147/jir.s340477] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023] Open
Abstract
Background Inflammatory response took part in the progression of tumor and was regarded as the hallmark of cancer. However, the prognostic relationship between osteosarcoma and inflammatory response-associated genes (IRGs) was unclear. This research aimed to explore the correlations between osteosarcoma prognosis and IRG signature. Methods The inflammatory response-associated differentially expressed messenger RNAs (DEmRNAs) were screened out through Gene Expression Omnibus (GEO) and Molecular Signature Database (MSigDB) databases. Univariate and multivariate cox regression analyses were utilized to construct the IRG signature. The prognostic value of signature was investigated through Kaplan–Meier (KM) survival curve and nomogram. DEmRNAs among high and low inflammatory response-associated risks were identified and functional enrichment analyses were conducted. ESTIMATE, CIBERSORT and single-sample gene set enrichment analyses (ssGSEA) were implied to reveal the alterations in immune infiltration. All the above results were validated in Target database. The expression of IRGs was also validated in different cell lines by quantitative real-time PCR (qRT-PCR) and osteosarcoma patient samples by immunohistochemistry. Results The IRG signature that consisted of two genes (MYC, CLEC5A) was established. In training and validation datasets, patients with lower risk scores survived longer and the IRG signature was confirmed as the independent prognostic factor in osteosarcoma. The nomogram was constructed and the calibration curves demonstrated the reliability of this model. Functional analysis of risk score-associated DEmRNAs indicated that immune-related pathways and functions were significantly enriched. ssGSEA revealed that 14 immune cells and 11 immune functions were significantly dysregulated. The qRT-PCR results indicated IRGs were significantly differently expressed in osteosarcoma and osteoblast cell lines. The immunohistochemistry analyses of patients’ samples revealed the same result. Conclusion The novel osteosarcoma inflammatory response-associated prognostic signature was established and validated in this study. This model could serve as the biomarker and therapeutic target for osteosarcoma in the future.
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Affiliation(s)
- Yucheng Fu
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Guoyu He
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Zhuochao Liu
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Jun Wang
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Zhusheng Zhang
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Qiyuan Bao
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Junxiang Wen
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Zhijian Jin
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Weibin Zhang
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
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Zhou X, Liu M, Deng G, Chen L, Sun L, Zhang Y, Luo C, Tang J. lncRNA LOC102724169 plus cisplatin exhibit the synergistic anti-tumor effect in ovarian cancer with chronic stress. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:294-309. [PMID: 33850634 PMCID: PMC8010577 DOI: 10.1016/j.omtn.2021.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/02/2021] [Indexed: 12/27/2022]
Abstract
Chronic stress has been proven to accelerate the development and progression of ovarian cancer, but the underlying molecular mechanisms have not been fully elucidated. In a combination survey of ovarian cancer with chronic stress (OCCS) mouse models and high-throughput sequencing, a key lncRNA named LOC102724169 on chromosome 6q27 has been identified, which functions as a dominant tumor suppressor in OCCS. Transcriptionally regulated by CCAAT enhancer binding protein (CEBP) beta (CEBPB), LOC102724169 shows low expression and correlates with poor progression-free survival (PFS) in OCCS patients. LOC102724169 is an instructive molecular inhibitor of malignancy of ovarian cancer cells, which is necessary to improve the curative effect of cisplatin therapy on ovarian cancer. This function stems from the inactivation of molecules in phosphatidylinositol 3-kinase (PI3K)/AKT signaling, repressing MYB expression and retaining the responsiveness of cancer cells to cisplatin. These findings provide a mechanistic understanding of the synergistic anti-tumor purpose of LOC102724169 as a bona fide tumor suppressor, enhancing the therapeutic effect of cisplatin. The new regulatory model of “lncRNA-MYB” provides new perspectives for LOC102724169 as a chronic stress-related molecule and also provides mechanistic insight into exploring the cancer-promoting mechanism of MYB in OCCS, which may be a promising therapeutic strategy for ovarian cancer.
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Affiliation(s)
- Xiaofang Zhou
- Department of Gynecologic Oncology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, P.R. China
| | - Mu Liu
- Department of Gynecologic Oncology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, P.R. China
| | - Guanming Deng
- Department of Gynecology and Obstetrics, Zhuhai Center for Maternal and Child Health Care, Zhuhai 519001, P.R. China
| | - Le Chen
- Department of Gynecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, P.R. China
| | - Lijuan Sun
- Department of Gynecology and Obstetrics, Shaoyang Central Hospital, Shaoyang 422000, P.R. China
| | - Yun Zhang
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, P.R. China
| | - Chenhui Luo
- Department of the Animal Lab, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, P.R. China
| | - Jie Tang
- Department of Gynecologic Oncology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, P.R. China.,Hunan Gynecologic Cancer Research Center, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, P.R. China
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11
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Su M, Qiao KY, Xie XL, Zhu XY, Gao FL, Li CJ, Zhao DQ. Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma. Front Genet 2021; 11:615680. [PMID: 33613623 PMCID: PMC7890365 DOI: 10.3389/fgene.2020.615680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2020] [Indexed: 12/19/2022] Open
Abstract
Analysis of single-cell RNA sequencing (scRNA-seq) data of immune cells from the tumor microenvironment (TME) may identify tumor progression biomarkers. This study was designed to investigate the prognostic value of differentially expressed genes (DEGs) in intrahepatic cholangiocarcinoma (ICC) using scRNA-seq. We downloaded the scRNA-seq data of 33,991 cell samples, including 17,090 ICC cell samples and 16,901 ICC adjacent tissue cell samples regarded as normal cells. scRNA-seq data were processed and classified into 20 clusters. The immune cell clusters were extracted and processed again in the same way, and each type of immune cells was divided into several subclusters. In total, 337 marker genes of macrophages and 427 marker genes of B cells were identified by comparing ICC subclusters with normal subclusters. Finally, 659 DEGs were obtained by merging B cell and macrophage marker genes. ICC sample clinical information and gene expression data were downloaded. A nine-prognosis-related-gene (PRG) signature was established by analyzing the correlation between DEGs and overall survival in ICC. The robustness and validity of the signature were verified. Functional enrichment analysis revealed that the nine PRGs were mainly involved in tumor immune mechanisms. In conclusion, we established a PRG signature based on scRNA-seq data from immune cells of patients with ICC. This PRG signature not only reflects the TME immune status but also provides new biomarkers for ICC prognosis.
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Affiliation(s)
- Miao Su
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.,Department of Gastroenterology, Hengshui People's Hospital, Hengshui, China
| | - Kuang-Yuan Qiao
- Basic Medical College, Hebei Medical University, Shijiazhuang, China
| | - Xiao-Li Xie
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xin-Ying Zhu
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.,Department of Gastroenterology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Fu-Lai Gao
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chang-Juan Li
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Dong-Qiang Zhao
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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12
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Wang F, Qin G, Liu J, Wang X, Ye B. Bio-analytical Identification of Key Genes that Could Contribute to the Progression and Metastasis of Osteosarcoma. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200801014939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Osteosarcoma (OS) is one of the most common primary malignant bone
tumors in children and adolescents. OS metastasis has been a challenge in the treatment of OS. The
present study screened progression related genes in OS by analyzing a public dataset GSE42352,
and identified 691 up-regulated and 945 down-regulated genes in advanced stage OS compared to
early-stage OS samples.
Methods:
Protein-protein interaction (PPI) networks were further employed to reveal the
interaction among these genes. Bioinformatics analysis showed that progression related differently
expressed genes (DEGs) were significantly associated with the regulation of cell proliferation and
metabolisms.
Results:
This study revealed that progression related DEGs were dysregulated in metastatic OS
compared to non-metastatic OS samples. Further analysis showed CSF1R, CASP1, CD163,
AP1B1, LAPTM5, PEX19, SLA, STAB1, YWHAH, PLCB2, and GPR84 were associated with the
metastasis-free survival time in patients with OS.
Conclusions:
These findings provided novel information for us to understand the mechanisms
underlying the progression and metastasis of OS.
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Affiliation(s)
- Fei Wang
- Department of Orthopedics, China-Japan Union Hospital Jilin University, Changchun, Jilin,China
| | - Guoqing Qin
- Department of Orthopedics, Jilin Disabled Persons' Rehabilitation Center, (Jilin Chunguang Rehabilitation Hospital), Changchun, Jilin,China
| | - Junzhi Liu
- Quality Control Department, China-Japan Union Hospital Jilin University, Changchun, Jilin,China
| | - Xiunan Wang
- Department of Orthopedics, The 964th Hospital of the PLA Joint Logistics Support Force, No. 4799 Xi 'an Road, Lvyuan District, Changchun City, Jilin Province,China
| | - Baoguo Ye
- Department of Anesthesiology, China-Japan Union Hospital Jilin University, Changchun, Jilin,China
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13
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Transcription Factor CEBPB Inhibits the Expression of the Human HTR1A by Binding to 5' Regulatory Region in Vitro. Genes (Basel) 2019; 10:genes10100802. [PMID: 31614865 PMCID: PMC6827163 DOI: 10.3390/genes10100802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/11/2019] [Accepted: 10/09/2019] [Indexed: 01/21/2023] Open
Abstract
This study identified a transcription factor that might bind to the 5′ regulatory region of the HTR1A and explored the potential effect on 5-HT1A receptor expression. Based on JASPAR predictions, the binding of the transcription factor was demonstrated using the electrophoretic mobility shift assay (EMSA). Vectors over-expressing the transcription factor were co-transfected into HEK-293 and SK-N-SH cells with the recombinant pGL3 vector, and relative fluorescence intensity was measured to determine regulatory activity. Additionally, the qRT-PCR and Western blot were also used to identify whether the transcription factor modulated the endogenous expression of 5-HT1A receptor. The results suggest that the transcription factor CCAA/T enhancer binding protein beta (CEBPB) likely binds to the −1219 to −1209 bp (ATG+1) region of the HTR1A. Two sequences located in the −722 to −372 bp and −119 to +99 bp were also identified. Although the effect of CEBPB on endogenous 5-HT1A receptor expression was not significant, it exhibited the strong inhibition on the relative fluorescence intensity and the mRNA level of HTR1A. CEBPB inhibited the human HTR1A expression by binding to the sequence −1219–−1209 bp. This is useful and informative for ascertaining the regulation of 5-HT1A receptor and mental diseases.
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14
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Lu J, Chen W, Liu H, Yang H, Liu T. Transcription factor CEBPB inhibits the proliferation of osteosarcoma by regulating downstream target gene CLEC5A. J Clin Lab Anal 2019; 33:e22985. [PMID: 31364785 PMCID: PMC6868409 DOI: 10.1002/jcla.22985] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/28/2022] Open
Abstract
Objective To screen the gene related to osteosarcoma (OS) metastasis and the molecular mechanism. Methods GEO database and R2 chip analysis platform were used to screen genes related to OS metastasis. UCSC gene browser was used to find the transcription factor (TF) of CLEC5A. The mRNA level and protein expression of CLEC5A in OS tissues and normal tissues were determined by RT‐PCR and Western blotting, respectively. OS cell lines MG‐63 were transfected with CEBPB recombinant plasmid. After transfection, the expression of CLEC5A in MG‐63 cells was determined and the cell proliferation situation was determined by clone formation assay. Results Three genes CLEC5A, ALOX5AP, and RNASE3 were obtained, and CLEC5A has the highest correlation with OS. CLEC5A has screened the gene related to OS metastasis, and CEBPB can be taken as TF regulating downstream gene CLEC5A. CEBPB can regulate the downstream CLEC5A as transcription factor. The relative mRNA level and protein expression of CLEC5A in OS tissues were significantly higher than those in normal tissues. CLEC5A can prevent OS metastasis. Transfection of CEBPB increased the expression of CLEC5A in MG‐63 cells and also inhibited the proliferation of OS. Conclusion CEBPB can inhibit the proliferation of OS cells via regulating the expression of CLEC5A.
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Affiliation(s)
- Jianhua Lu
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Weikai Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hao Liu
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huilin Yang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Tao Liu
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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