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Liu N, Jiang Y, Chen S, Pan F, Tang Y, Tan X. miRNA-27b-3p/TPX2 Axis Regulates Clear Cell Renal Cell Carcinoma Cell Proliferation, Invasion and Migration. Crit Rev Eukaryot Gene Expr 2024; 34:27-39. [PMID: 37824390 DOI: 10.1615/critreveukaryotgeneexpr.2023048827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
There is a wide variety of cancer cells that can be linked to the presence of TPX2. However, there is not a lot of evidence regarding its role in the development and maintenance of clear cell renal cell carcinoma (ccRCC). In our study, bioinformatics analysis was performed to obtain differentially expressed mRNAs and miR-NAs in ccRCC. Survival curves predicted correlation of TPX2 expression with patient survival. The upstream regulatory miRNA of TPX2 was predicted to be miRNA-27b-3p through database, and dual luciferase assay verified the targeted relationship. qRT-PCR and Western blot were employed for examination of TPX2 mRNA and protein expression in ccRCC cells. Proliferation, invasion, migration and cell cycle were detected by CCK-8, colony formation, wound healing, Transwell, and flow cytometry assays. The results showed that TPX2 showed very high expression in ccRCC, and patients with higher TPX2 expression had shorter relative survival. Low miRNA-27b-3p expression was found in ccRCC. Knockdown of TPX2 or forced expression of miRNA-27b-3p in ccRCC cells inhibited cell proliferation, migration, invasion, and arrested cell division in G0/G1 phase. Dual luciferase reporter presented that miRNA-27b-3p targeted TPX2 to inhibit its expression. Rescue experiments demonstrated that the miRNA-27b-3p/ TPX2 axis affected the biological functions of ccRCC cells. Concurrent overexpression of miRNA-27b-3p and TPX2 inhibited the facilitating effect of TPX2 on ccRCC cell growth. The results revealed novel regulatory mechanisms involved in ccRCC progression, hoping that it may spark an insight for later discovery about the new therapeutic targets for ccRCC.
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Affiliation(s)
- Nana Liu
- Oncology Department, People's Hospital of Chongqing Hechuan, Chongqing 401520, China
| | - Yicheng Jiang
- Oncology Department, People's Hospital of Chongqing Hechuan, Chongqing 401520, China
| | - Shiyuan Chen
- Oncology Department, People's Hospital of Chongqing Hechuan, Chongqing 401520, China
| | - Fang Pan
- Oncology Department, People's Hospital of Chongqing Hechuan, Chongqing 401520, China
| | - Yao Tang
- Oncology Department, People's Hospital of Chongqing Hechuan, Chongqing 401520, China
| | - Xingping Tan
- Oncology Department, People's Hospital of Chongqing Hechuan, Chongqing 401520, China
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Lu M, Xiao L, Xu B, Gao Q. Identification of Novel Genes and Associated Drugs in Advanced Clear Cell Renal Cell Carcinoma by Bioinformatic Methods. TOHOKU J EXP MED 2022; 258:79-90. [PMID: 35896362 DOI: 10.1620/tjem.2022.j059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Meiqi Lu
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University
| | - Liangxiang Xiao
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University
| | - Bo Xu
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University
| | - Qing Gao
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University.,The Third Clinical Medical College, Fujian Medical University
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Wu S, He H, Huang J, Jiang S, Deng X, Huang J, Chen Y, Jiang Y. FMR1 is identified as an immune-related novel prognostic biomarker for renal clear cell carcinoma: A bioinformatics analysis of TAZ/YAP. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:9295-9320. [PMID: 35942760 DOI: 10.3934/mbe.2022432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
WW domain-containing transcription regulator 1 (TAZ, or WWTR1) and Yes-associated protein 1 (YAP) are both important effectors of the Hippo pathway and exhibit different functions. However, few studies have explored their co-regulatory mechanisms in kidney renal clear cell carcinoma (KIRC). Here, we used bioinformatics approaches to evaluate the co-regulatory roles of TAZ/YAP and screen novel biomarkers in KIRC. GSE121689 and GSE146354 were downloaded from the GEO. The limma was applied to identify the differential expression genes (DEGs) and the Venn diagram was utilized to screen co-expressed DEGs. Co-expressed DEGs obtained the corresponding pathways through GO and KEGG analysis. The protein-protein interaction (PPI) network was constructed using STRING. The hub genes were selected applying MCODE and CytoHubba. GSEA was further applied to identify the hub gene-related signaling pathways. The expression, survival, receiver operating character (ROC), and immune infiltration of the hub genes were analyzed by HPA, UALCAN, GEPIA, pROC, and TIMER. A total of 51 DEGs were co-expressed in the two datasets. The KEGG results showed that the enriched pathways were concentrated in the TGF-β signaling pathway and endocytosis. In the PPI network, the hub genes (STAU2, AGO2, FMR1) were identified by the MCODE and CytoHubba. The GSEA results revealed that the hub genes were correlated with the signaling pathways of metabolism and immunomodulation. We found that STAU2 and FMR1 were weakly expressed in tumors and were negatively associated with the tumor stages. The overall survival (OS) and disease-free survival (DFS) rate of the high-expressed group of FMR1 was greater than that of the low-expressed group. The ROC result exhibited that FMR1 had certainly a predictive ability. The TIMER results indicated that FMR1 was positively correlated to immune cell infiltration. The abovementioned results indicated that TAZ/YAP was involved in the TGF-β signaling pathway and endocytosis. FMR1 possibly served as an immune-related novel prognostic gene in KIRC.
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Affiliation(s)
- Sufang Wu
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha 410013, Hunan, China
| | - Hua He
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha 410013, Hunan, China
| | - Jingjing Huang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha 410013, Hunan, China
| | - Shiyao Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha 410013, Hunan, China
| | - Xiyun Deng
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha 410013, Hunan, China
| | - Jun Huang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuanbing Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yiqun Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha 410013, Hunan, China
- School of Medicine, Hunan Normal University, Changsha 410013, Hunan, China
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Meng F, Xiao Y, Xie L, Liu Q, Qian K. Diagnostic and prognostic value of ABC transporter family member ABCG1 gene in clear cell renal cell carcinoma. Channels (Austin) 2021; 15:375-385. [PMID: 33825659 PMCID: PMC8032227 DOI: 10.1080/19336950.2021.1909301] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 12/24/2022] Open
Abstract
As the most common histologic subtype of renal cancer, clear cell renal cell carcinoma (ccRCC) poses a serious threat to public health. However, there are no specific molecular-targeted drugs for ccRCC at present. Human ATP-binding cassette (ABC) transporter family plays an important role in homeostasis maintenance. This study aimed to evaluate the potential diagnostic value of ABC genes in ccRCC. A total of 952 samples of ccRCC patients (707) and controls (245) from three different datasets were included for analysis. Receiver operating characteristic analysis and t-test were used to analyze the differential expression of ABC genes in ccRCC patients and control samples at mRNA level during screening and validations. The Cancer Genome Atlas (TCGA-ccRCC) dataset was utilized to investigate the correlation between ABC genes expression and prognostic value in ccRCC. We then investigated the interactions between ABCG1 and proteins in the Comparative Toxicogenomics Database (CTD). Finally, we found that ATP-binding cassette transporter G member 1 (ABCG1) was over-expressed in ccRCC patients compared with healthy samples at mRNA level. Cox regression analysis and Kaplan-Meier analysis showed that ccRCC patients with high ABCG1 expression had better overall survival (OS) than those patients with low expression (hazard ratio (HR) = 0.662, p = 0.007). This study demonstrated that ABCG1 is a potential diagnostic and prognostic biomarker in ccRCC and discussed the molecular mechanisms underlying the relationship between ccRCC and ABCG1, which might provide guidance for better management and treatment of ccRCC in the future.
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MESH Headings
- Humans
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/diagnosis
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/diagnosis
- ATP Binding Cassette Transporter, Subfamily G, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 1/metabolism
- Prognosis
- Male
- Female
- Middle Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Gene Expression Regulation, Neoplastic
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Affiliation(s)
- Fucheng Meng
- Department of Infection Control, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yafei Xiao
- Department of Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Longxiang Xie
- Department of Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Qiao Liu
- Department of Pediatric Dentistry, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Keli Qian
- Department of Infection Control, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Peng Q, Shen Y, Fu K, Dai Z, Jin L, Yang D, Zhu J. Artificial intelligence prediction model for overall survival of clear cell renal cell carcinoma based on a 21-gene molecular prognostic score system. Aging (Albany NY) 2021; 13:7361-7381. [PMID: 33686949 PMCID: PMC7993746 DOI: 10.18632/aging.202594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/14/2021] [Indexed: 01/03/2023]
Abstract
We developed and validated a new prognostic model for predicting the overall survival in clear cell renal cell carcinoma (ccRCC) patients. In this study, artificial intelligence (AI) algorithms including random forest and neural network were trained to build a molecular prognostic score (mPS) system. Afterwards, we investigated the potential mechanisms underlying mPS by assessing gene set enrichment analysis, mutations, copy number variations (CNVs) and immune cell infiltration. A total of 275 prognosis-related genes were identified, which were also differentially expressed between ccRCC patients and healthy controls. We then constructed a universal mPS system that depends on the expression status of only 21 of these genes by applying AI-based algorithms. Then, the mPS were validated by another independent cohort and demonstrated to be applicable to ccRCC subsets. Furthermore, a nomogram comprising the mPS score and several independent variables was established and proved to effectively predict ccRCC patient prognosis. Finally, significant differences were identified regarding the pathways, mutated genes, CNVs and tumor-infiltrating immune cells among the subgroups of ccRCC stratified by the mPS system. The AI-based mPS system can provide critical prognostic prediction for ccRCC patients and may be useful to inform treatment and surveillance decisions before initial intervention.
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Affiliation(s)
- Qiliang Peng
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Radiotherapy and Oncology, Soochow University, Suzhou, China
| | - Yi Shen
- Department of Radiation Oncology, The Affiliated Suzhou Science and Technology Town Hospital of Nanjing Medical University, Suzhou, China
| | - Kai Fu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zheng Dai
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lu Jin
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Dongrong Yang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jin Zhu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Sekino Y, Han X, Kobayashi G, Babasaki T, Miyamoto S, Kobatake K, Kitano H, Ikeda K, Goto K, Inoue S, Hayashi T, Teishima J, Sakamoto N, Sentani K, Oue N, Yasui W, Matsubara A. BUB1B Overexpression Is an Independent Prognostic Marker and Associated with CD44, p53, and PD-L1 in Renal Cell Carcinoma. Oncology 2021; 99:240-250. [PMID: 33588420 DOI: 10.1159/000512446] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION BUB1 mitotic checkpoint serine/threonine kinase B encoded by BUB1B gene is a member of the spindle assembly checkpoint family. Several reports have demonstrated that overexpression of BUB1B is associated with cancer progression and prognosis. OBJECTIVE This study aims to clarify the expression and function of BUB1B in renal cell carcinoma (RCC). METHODS The expression of BUB1B was determined using immunohistochemistry and bioinformatics analysis in RCC. The effects of BUB1B knockdown on cell growth and invasion were evaluated. We analyzed the interaction between BUB1B, cancer stem cell markers, p53, and PD-L1 in RCC. RESULTS In 121 cases of RCC, immunohistochemistry showed that 30 (25%) of the RCC cases were positive for BUB1B. High BUB1B expression was significantly correlated with high nuclear grade, T stage, and M stage. A Kaplan-Meier analysis showed that the high expression of BUB1B was associated with poor overall survival after nephrectomy. High BUB1B expression was associated with CD44, p53, and PD-L1 in RCC. Knockdown of BUB1B suppressed cell growth and invasion in RCC cell lines. Knockdown of BUB1B also suppressed the expression of CD44 and increased the expression of phospho-p53 (Ser15). In silico analysis showed that BUB1B was associated with inflamed CD8+, exhausted T-cell signature, IFN-γ signature, and the response to nivolumab. CONCLUSION These results suggest that BUB1B plays an oncogenic role and may be a promising predictive biomarker for survival in RCC.
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Affiliation(s)
- Yohei Sekino
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan,
| | - Xiangrui Han
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Go Kobayashi
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takashi Babasaki
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shunsuke Miyamoto
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kohei Kobatake
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroyuki Kitano
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenichiro Ikeda
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Keisuke Goto
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shogo Inoue
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tetsutaro Hayashi
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Jun Teishima
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Naoya Sakamoto
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Naohide Oue
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Wataru Yasui
- Department of Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akio Matsubara
- Department of Urology, Hiroshima General Hospital, Hatsukaichi, Japan
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