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Bai Y, Qu D, Lu D, Li Y, Zhao N, Cui G, Li X, Sun X, Sun H, Zhao L, Li Q, Zhang Q, Han T, Wang S, Yang Y. Pan-cancer landscape of abnormal ctDNA methylation across human tumors. Cancer Genet 2022; 268-269:37-45. [PMID: 36152512 DOI: 10.1016/j.cancergen.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 08/25/2022] [Accepted: 09/12/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND The aim of this paper is to explore the correlation between circulating tumor DNA (ctDNA) methylation and mutations and its value in clinical early cancer screening. METHODS We performed target region methylation sequencing and genome sequencing on plasma samples. Methylation models to distinguish cancer from healthy individuals have been developed using hypermethylated genes in tumors and validated in training set and prediction set. RESULTS We found that patients with cancer had higher levels of ctDNA methylation compared to healthy individuals. The level of ctDNA methylation in cell cycle, p53, Notch pathway in pan-cancer was significantly correlated with the number of mutations, and mutation frequency. Methylation burden in some tumors was significantly correlated with tumor mutational burden (TMB), microsatellite instability (MSI) and PD-L1. The ctDNA methylation differences in cancer patients were mainly concentrated in the Herpes simplex virus 1 infection pathway. The area under curve (AUC) of the training and prediction sets of the methylation model distinguishing cancer from healthy individuals were 0.93 and 0.92, respectively. CONCLUSION Our study provides a landscape of methylation levels of important pathways in pan-cancer. ctDNA methylation significantly correlates with mutation type, frequency and number, providing a reference for clinical application of ctDNA methylation in early cancer screening.
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Affiliation(s)
- Yun Bai
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Di Qu
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Dan Lu
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Yiwen Li
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Ning Zhao
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Guanghua Cui
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xue Li
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiaoke Sun
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Huaibo Sun
- Genecast Biotechnology Co., Ltd, Wuxi 214104, China
| | - Lihua Zhao
- Genecast Biotechnology Co., Ltd, Wuxi 214104, China
| | - Qingyuan Li
- Genecast Biotechnology Co., Ltd, Wuxi 214104, China
| | - Qi Zhang
- Genecast Biotechnology Co., Ltd, Wuxi 214104, China
| | | | - Song Wang
- Department of Medical Oncology, Mudanjiang Cancer Hospital, Mudanjiang 157009, China.
| | - Yu Yang
- Department of Medical Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China.
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Chen Z, Tang W, Ye W, Song L, Chen Z. ADAMTS9-AS2 regulates PPP1R12B by adsorbing miR-196b-5p and affects cell cycle-related signaling pathways inhibiting the malignant process of esophageal cancer. Cell Cycle 2022; 21:1710-1725. [PMID: 35503407 PMCID: PMC9302527 DOI: 10.1080/15384101.2022.2067675] [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] [Indexed: 11/03/2022] Open
Abstract
This study explored the mechanism that ADAMTS9-AS2/miR-196b-5p/PPP1R12B/cell cycle pathway axis in inhibiting the malignant progression of esophageal cancer (EC), providing a new idea for targeted molecular therapy of EC. The expression data of EC tissue were acquired from TCGA database. The target lncRNA, downstream miRNA and its target gene were determined by bioinformatics analysis. ADAMTS9-AS2, miR-196b-5p and PPP1R12B levels in EC tissue and cells were assayed through qRT-PCR. Western blot was applied to assess protein level of PPP1R12B in cells and tissues, as well as protein expression of CDK1, cyclin A2, cyclin B1 and Plk1 in EC cells. Cell proliferation was assayed via CCK-8 assay. Cell cycle distribution was analyzed by flow cytometry. Cell migratory and invasive abilities were measured through scratch healing and transwell assays. Pearson correlation analysis was utilized to analyze relationship among ADAMTS9-AS2, miR-196b-5p and PPP1R12B. RIP was introduced to assess binding among the three. Dual-luciferase assay was utilized to verify targeted binding sites. The tumor formation in nude mice assay was utilized to detect tumorigenesis of EC cells in vivo. ADAMTS9-AS2 was significantly lowly expressed while miR-196b-5p was increased in EC tissue and cells. ADAMTS9-AS2 bound to miR-196b-5p and constrained its expression. Overexpressed ADAMTS9-AS2 inhibited EC cell malignant progression via downregulating miR-196b-5p, while overexpressed miR-196b-5p reversed this inhibitory effect. ADAMTS9-AS2 modulated PPP1R12B level by competitively inhibiting miR-196b-5p. PPP1R12B played a modulatory role in EC by inhibiting cell cycle pathway. Overexpressed ADAMTS9-AS2 regulated the tumor-forming ability of EC cells in vivo through miR-196b-5p/PPP1R12B/cell cycle signaling pathway axis. ADAMTS9-AS2 downregulated PPP1R12B by adsorbing miR-196b-5p, so as to regulate the cell cycle signaling pathway to inhibit EC malignant progression.
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Affiliation(s)
- Zhao Chen
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Weijian Tang
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Weiwen Ye
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Lijiang Song
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhoumiao Chen
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
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Liang D, Tuo X, Wang Q, Zhao L, Zhang K, Wang Y, Feng X, Yin P, Guo L, Liu Y, Wang L, Han L, An R, Li Q. Near-Infrared Fluorescent Agent for In Vitro Screening of Endometrial Cancer and Precancerous Lesions. Front Oncol 2021; 11:713583. [PMID: 34277456 PMCID: PMC8281888 DOI: 10.3389/fonc.2021.713583] [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: 05/24/2021] [Accepted: 06/22/2021] [Indexed: 11/30/2022] Open
Abstract
The lack of cytopathologists delays the advancement of screening for endometrial cancer. It was urgent to develop a new dye for rapid diagnosis. Our study aimed to synthesize a targeted folate receptor-α near-infrared (NIR) fluorescent agent, folic acid-zwitterionic NIR fluorophore (ZW-FA), and explore the feasibility for screening of endometrial cancer and precancerous change. Folic acid was conjugated with zwitterionic NIR fluorophore. The preparation of ZW-FA was validated by 1H NMR, mass spectrometric, ultraviolet spectra and fluorescence spectra. ZW-FA was incubated with endometrial cytology samples obtained from patients who underwent dilation and curettage or total hysterectomy. Diagnostic utility was calculated by applying laser confocal microscope, Image-J and statistical models, such as enumeration, receiver operating characteristic curve, logistic regression, support vector machine and decision tree were used. The purity of ZW-FA was > 95% determined by 1H NMR. ZW-FA had the strongest absorption peak at 633 nm in ultraviolet spectra. Photostability of ZW-FA was over 8 hours. In clinical validation, a total of 92 patients were enrolled. The cut-off value of ZW-FA was 49 in enumeration, which was used to distinguish the type of samples. Indicators about diagnostic utility are as follows: sensitivity 90.77%, specificity 62.96%, false-positive rate 37.04%, false-negative rate 9.23%, positive predictive value 85.51% and negative predictive value 73.91%. The samples processed by ZW-FA did not affect further Hematoxylin-Eosin staining and pathological diagnosis. It was an effective cytologic strategy for in vitro diagnosis of endometrial cancer and precancerous change by using ZW-FA.
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Affiliation(s)
- Dongxin Liang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqian Tuo
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Qing Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Lanbo Zhao
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Kailu Zhang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yiran Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Xue Feng
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Panyue Yin
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Lin Guo
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yu Liu
- Department of Pathology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Lei Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Lu Han
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Ruifang An
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Qiling Li
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
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Ying X, Che X, Wang J, Zou G, Yu Q, Zhang X. CDK1 serves as a novel therapeutic target for endometrioid endometrial cancer. J Cancer 2021; 12:2206-2215. [PMID: 33758599 PMCID: PMC7974891 DOI: 10.7150/jca.51139] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Endometrial cancer (EC) is one of the most common and prevalent gynecologic malignancies worldwide. The aim of this study was to identify a novel therapeutic target for endometrioid endometrial cancer. Materials and Methods: Bioinformatic analysis was performed and CDK1 was screen out as one of the hub genes in the pathogenesis of EC. Immunohistochemistry was used to verify the expression of CDK1 in endometrial cancer tissue. Cell viability and colony formation were used to study the effects of CDK1 on the proliferation and colony formation of endometrial cancer cells in vitro. Apoptosis and cell cycle assays were used to elucidate the mechanism of CDK1 affecting cell proliferation. Tumor xenograft transplantation assay was performed to show the effects of CDK1 on the growth of endometrial cancer cells in vivo. Results: CDK1 was over expressed in endometrioid endometrial cancer, and accumulation of cytoplasmic CDK1 was associated with histological grade of EC. CDK1 promoted endometrial cancer cell growth and colony formation in vitro. The inhibition of CDK1 activity induced cell apoptosis and caused G2/M phase arrest of cell cycle in endometrial cancer cells. The inhibition of CDK1 activity also inhibited endometrial cancer growth in xenograft models. Conclusion: CDK1 was involved in the pathogenesis of endometrioid endometrial cancer and provided a novel therapeutic target for endometrioid endometrial cancer.
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Affiliation(s)
- Xue Ying
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China, 310006
| | - Xuan Che
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China, 310006.,Jiaxing University Affiliated Women and Children Hospital, Jiaxing, Zhejiang, P.R. China, 314000
| | - Jianzhang Wang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China, 310006
| | - Gen Zou
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China, 310006
| | - Qin Yu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China, 310006
| | - Xinmei Zhang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China, 310006
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Zhang XH, Li BF, Ding J, Shi L, Ren HM, Liu K, Huang CC, Ma FX, Wu XY. LncRNA DANCR-miR-758-3p-PAX6 Molecular Network Regulates Apoptosis and Autophagy of Breast Cancer Cells. Cancer Manag Res 2020; 12:4073-4084. [PMID: 32581581 PMCID: PMC7269637 DOI: 10.2147/cmar.s254069] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Objective This study set out to probe into the effects of long non-coding RNA (LncRNA) differentiation antagonizing non-protein coding RNA (DANCR) on apoptosis and autophagy of breast cancer (BC) cells. Methods The expression levels of DANCR, miR-758-3p and paired box 6 (PAX6) in BC tissues and cell lines were detected. The transcription and protein levels of PAX6, apoptosis-related factors (caspase-3, caspase-9, Bax/Bcl-2), and autophagy-related factors (LC3B, Atg5, Beclin-1) in BC cells were detected. The cell proliferation, apoptosis, autophagy and the regulatory relationship between genes and target genes were analyzed. Results DANCR and PAX6 were up-regulated in BC tissues and cell lines, while miR-758-3p was opposite. Down-regulating DANCR inhibited the malignant proliferation of BC cells and also promoted apoptosis and autophagy, which showed that caspase-3, caspase-9, Bax/Bcl-2, LC3B, Atg5 transcription and protein levels increased, while Beclin-1 transcription and protein levels decreased. DANCR regulated miR-758-3p in a targeted manner, and its over-expression could weaken the anti-cancer effect of miR-758-3p on BC cells. In addition, miR-758-3p also directly targeted PAX6, and knocking down its expression could weaken the inhibitory effect of down-regulating PAK6 on BC cell apoptosis and autophagy. We also found that DANCR acted as a competitive endogenous RNA sponge miR-758-3p, thus regulating the PAX6 expression. Conclusion DANCR-miR-758-3p-PAX6 molecular network plays a key regulatory role in BC cell apoptosis and autophagy, which may provide reference for treating patients.
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Affiliation(s)
- Xian Hu Zhang
- Department of General Surgery, Suzhou First People's Hospital, Suzhou, Anhui 234000, People's Republic of China
| | - Bing Feng Li
- Department of General Surgery, Suzhou First People's Hospital, Suzhou, Anhui 234000, People's Republic of China
| | - Jie Ding
- Physical Examination Department, Suzhou Central Blood Station, Suzhou, Anhui 234000, People's Republic of China
| | - Lei Shi
- Department of General Surgery, Suzhou First People's Hospital, Suzhou, Anhui 234000, People's Republic of China
| | - Huo Ming Ren
- Department of General Surgery, Suzhou First People's Hospital, Suzhou, Anhui 234000, People's Republic of China
| | - Kui Liu
- Department of General Surgery, Suzhou First People's Hospital, Suzhou, Anhui 234000, People's Republic of China
| | - Chuan Cai Huang
- Department of General Surgery, Suzhou First People's Hospital, Suzhou, Anhui 234000, People's Republic of China
| | - Fu Xiao Ma
- Department of General Surgery, Suzhou First People's Hospital, Suzhou, Anhui 234000, People's Republic of China
| | - Xin Yao Wu
- Department of General Surgery, Suzhou First People's Hospital, Suzhou, Anhui 234000, People's Republic of China
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Zhou JW, Wang H, Sun W, Han NN, Chen L. ASPM is a predictor of overall survival and has therapeutic potential in endometrial cancer. Am J Transl Res 2020; 12:1942-1953. [PMID: 32509189 PMCID: PMC7270042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 04/11/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Endometrial carcinoma (EC) is one of the most common cancers in women, and its pathogenesis is complex. Abnormal spindle microtubule assembly (ASPM) is highly expressed in a variety of cancers and is related to poor clinical prognosis and recurrence. However, the role of ASPM in EC is still unclear. Our study was conducted to investigate the association of ASPM with tumour progression and prognosis in EC. METHODS The expression level of ASPM in EC patients was analysed by using the TCGA database and by using immunohistochemistry (IHC) to analyse EC patient samples. The relationship between ASPM expression and clinicopathological variables was analysed by the chi-square test. Survival curves were analysed by Kaplan-Meier survival analysis and log-rank test. Univariate and multivariate Cox regression analyses were performed to measure the prognosis of EC. The effects of ASPM on the proliferation, invasion and metastasis of EC cells (HEC-1A and Ishikawa) were analysed by MTT and Transwell assays. The effect of ASPM on the Wnt/β-catenin signalling pathway was detected by Western blotting. RESULTS ASPM was highly overexpressed in EC. Overexpression of ASPM was related to significantly worse overall survival (P<0.05) in EC patients. Univariate and multivariate Cox regression analyses suggested that upregulation of ASPM was related to poor prognosis in EC. Knockdown of ASPM inhibited the proliferation, migration and invasion of EC cells. ASPM knockdown suppressed the Wnt/β-catenin signalling pathway, while β-catenin overexpression reversed the effect of shASPM on cell activity. CONCLUSIONS ASPM acts as an independent predictor of clinical prognosis and serves as a potential target gene for EC therapy.
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Affiliation(s)
- Jing-Wei Zhou
- Department of Gynaecology, Jiangsu Province Hospital Nanjing 210000, P. R. China
| | - Hui Wang
- Department of Gynaecology, Jiangsu Province Hospital Nanjing 210000, P. R. China
| | - Wei Sun
- Department of Gynaecology, Jiangsu Province Hospital Nanjing 210000, P. R. China
| | - Nan-Nan Han
- Department of Gynaecology, Jiangsu Province Hospital Nanjing 210000, P. R. China
| | - Liang Chen
- Department of Gynaecology, Jiangsu Province Hospital Nanjing 210000, P. R. China
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Chen S, Shi F, Zhang W, Zhou Y, Huang J. miR-744-5p Inhibits Non-Small Cell Lung Cancer Proliferation and Invasion by Directly Targeting PAX2. Technol Cancer Res Treat 2020; 18:1533033819876913. [PMID: 31522607 PMCID: PMC6747846 DOI: 10.1177/1533033819876913] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Non-small cell lung cancer is one of the leading causes of cancer-related death worldwide. MicroRNAs have been characterized as critical regulators for cancer progression including non-small cell lung cancer. This work explored microRNA-744-5p expression in non-small cell lung cancer cell lines and normal cell line using quantitative real-time polymerase chain reaction. Connection of microRNA-744-5p and paired box 2 was analyzed with bioinformatic analysis, luciferase activity reporter assay, and Western blot. Effects of microRNA-744-5p or paired box 2 expression on non-small cell lung cancer cell behaviors were analyzed using a series of in vitro experiments. MicroRNA-744-5p was found to have decreased expression in non-small cell lung cancer cell lines compared with normal cell line. Paired box 2 was identified as a direct target for microRNA-744-5p in non-small cell lung cancer. Overexpression of microRNA-744-5p inhibits non-small cell lung cancer cell proliferation, colony formation, and cell invasion in vitro through targeting paired box 2. The present study provided novel insights into the biological functions of microRNA-744-5p in non-small cell lung cancer.
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Affiliation(s)
- Shaolin Chen
- Emergency Department, Jinan University, The Second Clinical Medical College, Shenzhen, People's Republic of China
| | - Fei Shi
- Emergency Department, Jinan University, The Second Clinical Medical College, Shenzhen, People's Republic of China
| | - Weixing Zhang
- Emergency Critical Center, Peking University Shenzhen Hospital, Shenzhen, People's Republic of China
| | - Yuqi Zhou
- Division of Pulmonary and Critical Care, Department of Internal Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jing Huang
- Division of Pulmonary and Critical Care, Department of Internal Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
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Deng Y, Xie Q, Zhang G, Li S, Wu Z, Ma Z, He X, Gao Y, Wang Y, Kang X, Wang J. Slow skeletal muscle troponin T, titin and myosin light chain 3 are candidate prognostic biomarkers for Ewing's sarcoma. Oncol Lett 2019; 18:6431-6442. [PMID: 31807166 PMCID: PMC6876326 DOI: 10.3892/ol.2019.11044] [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: 03/16/2019] [Accepted: 09/17/2019] [Indexed: 11/29/2022] Open
Abstract
Ewing's sarcoma (ES) is a common malignant bone tumor in children and adolescents. Although great efforts have been made to understand the pathogenesis and development of ES, the underlying molecular mechanism remains unclear. The present study aimed to identify new key genes as potential biomarkers for the diagnosis, targeted therapy or prognosis of ES. mRNA expression profile chip data sets GSE17674, GSE17679 and GSE45544 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened using the R software limma package, and functional and pathway enrichment analyses were performed using the enrichplot package and GSEA software. The NetworkAnalyst online tool, as well as Cytoscape and its plug-ins cytoHubba and NetworkAnalyzer, were used to construct a protein-protein interaction network (PPI) and conduct module analysis to screen key (hub) genes. LABSO COX regression and overall survival (OS) analysis of the Hub genes were performed. A total of 211 DEGs were obtained by integrating and analyzing the three data sets. The functions and pathways of the DEGs were mainly associated with the regulation of small-molecule metabolic processes, cofactor-binding, amino acid, proteasome and ribosome biosynthesis in eukaryotes, as well as the Rac1, cell cycle and P53 signaling pathways. A total of one important module and 20 hub genes were screened from the PPI network using the Maximum Correlation Criteria algorithm of cytoHubba. LASSO COX regression results revealed that titin (TTN), fast skeletal muscle troponin T, skeletal muscle actin α-actin, nebulin, troponin C type 2 (fast), myosin light-chain 3 (MYL3), slow skeletal muscle troponin T (TNNT1), myosin-binding protein C1 slow-type, tropomyosin 3 and myosin heavy-chain 7 were associated with prognosis in patients with ES. The Kaplan-Meier curves demonstrated that high mRNA expression levels of TNNT1 (P<0.001), TTN (P=0.049), titin-cap (P=0.04), tropomodulin 1 (P=0.011), troponin I2 fast skeletal type (P=0.021) and MYL3 (P=0.017) were associated with poor OS in patients with ES. In conclusion, the DEGs identified in the present study may be key genes in the pathogenesis of ES, three of which, namely TNNT1, TTN and MYL3, may be potential prognostic biomarkers for ES.
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Affiliation(s)
- Yajun Deng
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Qiqi Xie
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Guangzhi Zhang
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Shaoping Li
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Zuolong Wu
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Zhanjun Ma
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Xuegang He
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Yicheng Gao
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Yonggang Wang
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Xuewen Kang
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Jing Wang
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Orthopedic Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
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9
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Webb Chasser AM, Johnson RW, Chamberlin HM. EGL-38/Pax coordinates development in the Caenhorhabditis elegans egg-laying system through EGF pathway dependent and independent functions. Mech Dev 2019; 159:103566. [PMID: 31398431 PMCID: PMC6855382 DOI: 10.1016/j.mod.2019.103566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/26/2019] [Accepted: 08/01/2019] [Indexed: 01/01/2023]
Abstract
Paired box (Pax) proteins function as regulators of coordinated development in organogenesis by controlling factors such as cell growth and differentiation necessary to organize multiple cell types into a single, cohesive organ. Previous work has suggested that Pax transcription factors may regulate diverse cell types through participation in inductive cell-to-cell signaling, which has not been well explored. Here we show that EGL-38, a Pax2/5/8 ortholog, coordinates differentiation of the C. elegans egg-laying system through separate autonomous and non-autonomous functions synchronized by the EGF pathway. We find that EGL-38 protein is expressed at the correct times to both participate in and respond to the EGF pathway specifying uterine ventral (uv1) cell fate, and that EGL-38 is required for uv1 expression of nlp-2 and nlp-7, which are both markers of and participants in uv1 identity. Additionally, we have separated uv1 cell placement and gene expression as distinct hallmarks of uv1 identity and specification, with different dependencies on EGL-38. The parallels between EGL-38 participation in cell signaling events and previous Pax studies argue that coordination of signaling and response to an inductive pathway may be a common feature of Pax protein function.
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Affiliation(s)
- Allison M Webb Chasser
- Department of Molecular Genetics, United States of America; Ohio State Biochemistry Graduate Program, United States of America
| | - Ryan W Johnson
- Department of Molecular Genetics, United States of America
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Liu L, Lin J, He H. Identification of Potential Crucial Genes Associated With the Pathogenesis and Prognosis of Endometrial Cancer. Front Genet 2019; 10:373. [PMID: 31105744 PMCID: PMC6499025 DOI: 10.3389/fgene.2019.00373] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022] Open
Abstract
Background and Objective Endometrial cancer (EC) is a common gynecological malignancy worldwide. Despite advances in the development of strategies for treating EC, prognosis of the disease remains unsatisfactory, especially for advanced EC. The aim of this study was to identify novel genes that can be used as potential biomarkers for identifying the prognosis of EC and to construct a novel risk stratification using these genes. Methods and Results An mRNA sequencing dataset, corresponding survival data and expression profiling of an array of EC patients were obtained from The Cancer Genome Atlas and Gene Expression Omnibus, respectively. Common differentially expressed genes (DEGs) were identified based on sequencing and expression as given in the profiling dataset. Pathway enrichment analysis of the DEGs was performed using the Database for Annotation, Visualization, and Integrated Discovery. The protein-protein interaction network was established using the string online database in order to identify hub genes. Univariate and multivariable Cox regression analyses were used to screen prognostic DEGs and to construct a prognostic signature. Survival analysis based on the prognostic signature was performed on TCGA EC dataset. A total of 255 common DEGs were found and 11 hub genes (TOP2A, CDK1, CCNB1, CCNB2, AURKA, PCNA, CCNA2, BIRC5, NDC80, CDC20, and BUB1BA) that may be closely related to the pathogenesis of EC were identified. A panel of 7 DEG signatures consisting of PHLDA2, GGH, ESPL1, FAM184A, KIAA1644, ESPL1, and TRPM4 were constructed. The signature performed well for prognosis prediction (p < 0.001) and time-dependent receiver-operating characteristic (ROC) analysis displayed an area under the curve (AUC) of 0.797, 0.734, 0.729, and 0.647 for 1, 3, 5, and 10-year overall survival (OS) prediction, respectively. Conclusion This study identified potential genes that may be involved in the pathophysiology of EC and constructed a novel gene expression signature for EC risk stratification and prognosis prediction.
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Affiliation(s)
- Li Liu
- Department of Obstetrics and Gynecology, Liuzhou Worker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Jiajing Lin
- Department of Obstetrics and Gynecology, Liuzhou Worker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Hongying He
- Department of Obstetrics and Gynecology, Liuzhou Worker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
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