1
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Blanchett R, Lau KH, Pfeifer GP. Homeobox and Polycomb target gene methylation in human solid tumors. Sci Rep 2024; 14:13912. [PMID: 38886487 PMCID: PMC11183203 DOI: 10.1038/s41598-024-64569-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
DNA methylation is an epigenetic mark that plays an important role in defining cancer phenotypes, with global hypomethylation and focal hypermethylation at CpG islands observed in tumors. These methylation marks can also be used to define tumor types and provide an avenue for biomarker identification. The homeobox gene class is one that has potential for this use, as well as other genes that are Polycomb Repressive Complex 2 targets. To begin to unravel this relationship, we performed a pan-cancer DNA methylation analysis using sixteen Illumina HM450k array datasets from TCGA, delving into cancer-specific qualities and commonalities between tumor types with a focus on homeobox genes. Our comparisons of tumor to normal samples suggest that homeobox genes commonly harbor significant hypermethylated differentially methylated regions. We identified two homeobox genes, HOXA3 and HOXD10, that are hypermethylated in all 16 cancer types. Furthermore, we identified several potential homeobox gene biomarkers from our analysis that are uniquely methylated in only one tumor type and that could be used as screening tools in the future. Overall, our study demonstrates unique patterns of DNA methylation in multiple tumor types and expands on the interplay between the homeobox gene class and oncogenesis.
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Affiliation(s)
- Reid Blanchett
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA
| | - Kin H Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA.
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2
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Han L, Wang Z, Li C, Fan M, Wang Y, Sun G, Dai G. Functional identification and prediction of lncRNAs in esophageal cancer. Comput Biol Med 2023; 165:107205. [PMID: 37611425 DOI: 10.1016/j.compbiomed.2023.107205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/29/2023] [Accepted: 06/25/2023] [Indexed: 08/25/2023]
Abstract
Esophageal cancer is a highly lethal malignancy with poor prognosis, and the identification of molecular biomarkers is crucial for improving diagnosis and treatment. Long non-coding RNAs (lncRNAs) have been shown to play important roles in the development and progression of esophageal cancer. However, due to the time cost of biological experiments, only a small number of lncRNAs related to esophageal cancer have been discovered. Currently, computational methods have emerged as powerful tools for identifying and characterizing lncRNAs, as well as predicting their potential functions. Therefore, this article proposes a transformer-based method for identifying esophageal cancer-related lncRNAs. Experimental results show that the AUC and AUPR of this method are superior to other comparison methods, with an AUC of 0.87 and an AUPR of 0.83, and the identified lncRNA targets are closely associated with esophageal cancer. We focus on the role of esophageal cancer-related lncRNAs in the immune microenvironment, and fully explore the functions of the target genes regulated by lncRNAs. Enrichment analysis shows that the predicted target genes are related to multiple pathways involved in the occurrence, development, and prognosis of esophageal cancer. This not only demonstrates the effectiveness of the method but also indicates the accuracy of the prediction results.
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Affiliation(s)
- Lu Han
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Zhikuan Wang
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Congyong Li
- Medical School of Chinese PLA, Beijing, China; Sixth Health Care Department, The Second Medical Center of PLA General Hospital, Beijing, China
| | - Mengjiao Fan
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Yanrong Wang
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Gang Sun
- Department of Gastroenterology and Hepatology, The First Medical Center of Chinese PLA General Hospital, Beijing, China.
| | - Guanghai Dai
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
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3
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Sharma S, Tyagi W, Tamang R, Das S. HDAC5 modulates SATB1 transcriptional activity to promote lung adenocarcinoma. Br J Cancer 2023; 129:586-600. [PMID: 37400677 PMCID: PMC10421875 DOI: 10.1038/s41416-023-02341-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/29/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Dysregulation of histone deacetylases has been linked to diverse cancers. HDAC5 is a histone deacetylase belonging to Class IIa family of histone deacetylases. Limited substrate repertoire restricts the understanding of molecular mechanisms underlying its role in tumorigenesis. METHODS We employed a biochemical screen to identify SATB1 as HDAC5-interacting protein. Coimmunoprecipitation and deacetylation assay were performed to validate SATB1 as a HDAC5 substrate. Proliferation, migration assay and xenograft studies were performed to determine the effect of HDAC5-SATB1 interaction on tumorigenesis. RESULTS Here we report that HDAC5 binds to and deacetylates SATB1 at the conserved lysine 411 residue. Furthermore, dynamic regulation of acetylation at this site is determined by TIP60 acetyltransferase. We also established that HDAC5-mediated deacetylation is critical for SATB1-dependent downregulation of key tumor suppressor genes. Deacetylated SATB1 also represses SDHA-induced epigenetic remodeling and anti-proliferative transcriptional program. Thus, SATB1 spurs malignant phenotype in a HDAC5-dependent manner. CONCLUSIONS Our study highlights the pivotal role of HDAC5 in tumorigenesis. Our findings provide key insights into molecular mechanisms underlying SATB1 promoted tumor growth and metastasis.
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Affiliation(s)
- Shalakha Sharma
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Witty Tyagi
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rohini Tamang
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjeev Das
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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4
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Luo Q, Zhou P, Chang S, Huang Z, Zeng X. Construction and validation of a prognostic model for colon adenocarcinoma based on bile acid metabolism-related genes. Sci Rep 2023; 13:12728. [PMID: 37543674 PMCID: PMC10404223 DOI: 10.1038/s41598-023-40020-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Colon adenocarcinoma (COAD), one of the common clinical cancers, exhibits high morbidity and mortality, and its pathogenesis and treatment are still underdeveloped. Numerous studies have demonstrated the involvement of bile acids in tumour development, while the potential role of their metabolism in the tumor microenvironment (TME) has not been explored. A collection of 481 genes related to bile acid metabolism were obtained, and The Cancer Genome Atlas-based COAD risk model was developed using the least absolute shrinkage selection operator (LASSO) regression analysis. The Gene Expression Omnibus dataset was used to validate the results. The predictive performance of the model was verified using column line plots, principal component analysis and receiver operating characteristic curves. Then, we analysed the differences between the high- and low-risk groups from training set based on clinical characteristics, immune cell infiltration, immune-related functions, chemotherapeutic drug sensitivity and immunotherapy efficacy. Additionally, we constructed a protein-protein interaction network to screen for target genes, which were further investigated in terms of differential immune cell distribution. A total of 234 bile acids-related differentially expressed genes were obtained between normal and tumour colon tissues. Among them, 111 genes were upregulated and 123 genes were down-regulated in the tumour samples. Relying on the LASSO logistic regression algorithm, we constructed a model of bile acid risk score, comprising 12 genes: CPT2, SLCO1A2, CD36, ACOX1, CDKN2A, HADH, GABRD, LEP, TIMP1, MAT1A, SLC6A15 and PPARGC1A. This model was validated in the GEO-COAD set. Age and risk score were observed to be independent prognostic factors in patients with COAD. Genes related to bile acid metabolism in COAD were closely related to bile secretion, intestinal transport, steroid and fatty acid metabolism. Furthermore, the high-risk group was more sensitive to Oxaliplatin than the low-risk group. Finally, the three target genes screened were closely associated with immune cells. We identified a set of 12 genes (CPT2, SLCO1A2, CD36, ACOX1, CDKN2A, HADH, GABRD, LEP, TIMP1, MAT1A, SLC6A15, and PPARGC1A) associated with bile acid metabolism and developed a bile acid risk score model using LASSO regression analysis. The model demonstrated good predictive performance and was validated using an independent dataset. Our findings revealed that the bile acid risk score were independent prognostic factors in COAD patients.
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Affiliation(s)
- Qinghua Luo
- Department of Anorectal Surgery, Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, China.
| | - Ping Zhou
- Department of Anorectal Surgery, Jiangxi Hospital of Integrated Traditional Chinese and Western Medicine, Nanchang, China
| | - Shuangqing Chang
- Department of Anorectal Surgery, Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, China
| | - Zhifang Huang
- Department of Anorectal Surgery, Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, China
| | - Xuebo Zeng
- Department of Brain Diseases, Shenzhen Pingle Orthopaedic Hospital, Shenzhen, China
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5
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Zhu Q, Xu H, Huang L, Luo J, Li H, Yang R, Liu X, Liu F. Identification and detection of plasma extracellular vesicles-derived biomarkers for esophageal squamous cell carcinoma diagnosis. Biosens Bioelectron 2023; 225:115088. [PMID: 36739741 DOI: 10.1016/j.bios.2023.115088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Esophageal cancer is a malignant tumor with two-thirds of patients having a local recurrence or distant metastasis. To date, diagnostic biomarkers with high sensitivity and specificity are lacking. Extracellular vesicles (EVs) have shown their potential values as disease biomarkers as they carry specific proteins and RNAs derived from cancer cells. In this study, we investigate ESCC precision diagnostics from the insights of circulating EVs, and integrate the ultrafast EV isolation approach (EXODUS) and ELISA for fast detection and screening of ESCC patients. First, we isolate and characterize the high-purity plasma EVs with EXODUS and identify 401 proteins and 372 proteins from ESCC patient and healthy individuals, respectively. Further looking into the differentially expressed proteins (DEPs) of ESCC patients and enriched KEGG pathways, we discover EV-CD14 as a potential diagnostic biomarker for ESCC, which has been further validated as a significantly differentially expressed protein by Western Blot and immunogold labelling TEM. For fast screening and detection of ESCC towards clinical applications, we apply ELISA method to diagnose ESCC from 60 clinical samples based on circulating EV-CD14, which shows a high AUC value up to 96.0% for detection of ESCC in a test set (30 samples), and displays a high accuracy rate up to 90% for prediction of ESCC in a screening test (30 samples). Our results suggest that the circulating EV-CD14 may highly be related to the initiation and progression of ESCC, providing a novel method for the diagnosis and prognosis of ESCC towards clinical translations.
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Affiliation(s)
- Qingfu Zhu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hao Xu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Liu Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Jiaxin Luo
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hengrui Li
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Rui Yang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiaoling Liu
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, China
| | - Fei Liu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
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6
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Bansal R, Saxena U. Integrative Analysis of Potential Biomarkers Involved in the Progression of Papillary Thyroid Cancer. Appl Biochem Biotechnol 2022; 195:2917-2932. [PMID: 36445679 DOI: 10.1007/s12010-022-04244-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 11/30/2022]
Abstract
This study aims to explore key prognostic and diagnostic biomarkers involved in the pathogenesis of papillary thyroid cancer (PTC) which is one of the most common endocrine cancers and whose occurrence is rapidly increasing. Papillary thyroid cancer datasets containing normal and tumor samples were collected from Gene Expression Omnibus. Protein-protein interaction (PPI) network for common upregulated differentially expressed genes (DEGs) was constructed, and hub genes were studied. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed to identify the vital biological behaviors and pathways involved in PTC. PPI network analysis demonstrated the interaction between 134 common upregulated DEGs, and top 15 pivotal genes with highest degree of connectivity were retrieved. Three of the hub genes (DPP4, ITGA2, FN1) were linked to the prognosis of PTC patients and considered clinically relevant core genes via survival analysis. We suggest that the identification of key genes associated with PTC development help us in understanding molecular mechanisms related to disease. These genes could also be considered the diagnostic biomarkers or as therapeutic targets in the future treatment for PTC.
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Affiliation(s)
- Ritu Bansal
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, 506004, Telangana, India
| | - Urmila Saxena
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, 506004, Telangana, India.
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7
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Feng J, Tang X, Song L, Zhou Z, Jiang Y, Huang Y. Potential biomarkers and immune characteristics of small bowel adenocarcinoma. Sci Rep 2022; 12:16204. [PMID: 36171259 PMCID: PMC9519963 DOI: 10.1038/s41598-022-20599-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/15/2022] [Indexed: 11/18/2022] Open
Abstract
Small bowel adenocarcinoma (SBA) is a gastrointestinal malignancy with low incidence but poor prognosis, and its pathogenesis is still unclear. This study aimed to explore potential disease-causing biomarkers of SBA. The gene expression datasets of SBA and normal samples were downloaded from the Gene Expression Omnibus database. First, differential gene expression analysis and weighted gene coexpression network analysis (WGCNA) were performed. Common genes (CGs) were obtained by intersection of differentially expressed genes (DEGs) and optimal modal genes of WGCNA. Subsequently, a protein‒protein interaction network was established to screen hub genes, and target genes were obtained by Lasso regression analysis of hub genes. An SBA risk prediction model was established based on target genes. The prediction accuracy of the model was evaluated by the area under the receiver operating characteristic curve (AUC). The levels of immune cell infiltration and activation of immune pathways were compared between SBA and normal samples using the "ggpubr" and "reshape2" packages. A total of 1058 DEGs were identified. WGCNA showed that the signature gene in the brown module was significantly associated with SBA (p = 7E−17), and 469 CGs were obtained. Four target genes (APOA4, APOB, COL1A2, FN1) were identified and showed excellent prediction of SBA risk (AUC = 0.965). In addition, active dendritic cells and macrophages showed higher infiltration levels in SBA. Meanwhile, the APC_co_stimulation pathway and parainflammation pathway were strongly active in SBA. Four target genes (APOA4, APOB, COL1A2, FN1) may be involved in the pathogenesis of small bowel adenocarcinoma.
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Affiliation(s)
- Jinggao Feng
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan, China.
| | - Xiayu Tang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan, China
| | - Liusong Song
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan, China
| | - Zhipeng Zhou
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan, China
| | - Yuan Jiang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan, China
| | - Yao Huang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan, China
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8
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Zhang XX, Luo JH, Wu LQ. FN1 overexpression is correlated with unfavorable prognosis and immune infiltrates in breast cancer. Front Genet 2022; 13:913659. [PMID: 36035176 PMCID: PMC9417469 DOI: 10.3389/fgene.2022.913659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/11/2022] [Indexed: 12/14/2022] Open
Abstract
Objective: To investigate the correlation of fibronectin 1 (FN1) expression with prognosis and tumor-infiltrating immune cells in breast cancer (BRCA). Methods: FN1 mRNA and protein expressions were analyzed through Tumor Immune Estimation Resource (TIMER), Gene Set Cancer Analysis (GSCA), Human Protein Atlas (HPA) databases, and immunohistochemical analysis. The clinicopathological characteristics and genetic factors affecting the FN1 mRNA expression were assessed by various public databases. Then, we analyzed the prognostic value of FN1 in BRCA by Kaplan-Meier plotter, receiver operating characteristic, and Cox regression analyses. Further, the UCSC Xena database was used to retrieve TCGA-BRCA expression profiles for functional enrichment analysis and immune cell infiltration analysis. The potential drugs for the BRCA patients with high- FN1 expression were identified using the connectivity map analysis. Results: FN1 was upregulated in BRCA tissues compared with normal tissues. High FN1 mRNA expression was correlated with poor clinical outcomes and had good performance in predicting the survival status of BRCA patients. Further, Cox regression analysis showed that FN1 was an independent prognostic factor for predicting the overall survival of patients with BRCA. Moreover, hypermethylation of FN1 contributed to a better prognosis for BRCA patients. Functional enrichment analyses revealed the ECM-receptor interaction pathway and focal adhesion as the common pathways. Moreover, FN1 showed a significant association with tumor-infiltrating immune cells and immune checkpoint inhibitors. Several drugs such as telmisartan, malotilate, and seocalcitol may have therapeutic effects in BRCA patients with high FN1 expression. Conclusion: FN1 might serve as a novel prognostic biomarker and a novel therapeutic target for BRCA. Besides, the association of FN1 with immune cells and immune checkpoint inhibitors may provide assistance for BRCA treatment.
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Affiliation(s)
- Xiu-Xia Zhang
- Department of Thyroid and Breast Surgery, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun-Hua Luo
- Department of Thyroid and Breast Surgery, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Li-Qiang Wu
- Department of Hematology, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, Zhejiang, China
- *Correspondence: Li-Qiang Wu,
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Liang J, Huang X, Li W, Hu Y. Identification and external validation of the hub genes associated with cardiorenal syndrome through time-series and network analyses. Aging (Albany NY) 2022; 14:1351-1373. [PMID: 35133974 PMCID: PMC8876909 DOI: 10.18632/aging.203878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
Cardiorenal syndrome (CRS), defined as acute or chronic damage to the heart or kidney triggering impairment of another organ, has a poor prognosis. However, the molecular mechanisms underlying CRS remain largely unknown. The RNA-sequencing data of the left ventricle tissue isolated from the sham-operated and CRS model rats at different time points were downloaded from the Gene Expression Omnibus (GEO) database. Genomic differences, protein–protein interaction networks, and short time-series analyses, revealed fibronectin 1 (FN1) and periostin (POSTN) as hub genes associated with CRS progression. The transcriptome sequencing data of humans obtained from the GEO revealed that FN1 and POSTN were both significantly associated with many different heart and kidney diseases. Peripheral blood samples from 20 control and 20 CRS patients were collected from the local hospital, and the gene expression levels of FN1 and POSTN were detected by real-time quantitative polymerase chain reaction. FN1 (area under the curve [AUC] = 0.807) and POSTN (AUC = 0.767) could distinguish CRS in the local cohort with high efficacy and were positively correlated with renal and heart damage markers, such as left ventricular ejection fraction. To improve the diagnostic ability, diagnosis models comprising FN1 and POSTN were constructed by logistic regression (F-Score = 0.718), classification tree (F-Score = 0.812), and random forest (F-Score = 1.000). Overall, the transcriptome data of CRS rat models were systematically analyzed, revealing that FN1 and POSTN were hub genes, which were validated in different public datasets and the local cohort.
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Affiliation(s)
- Jingjing Liang
- Department of Cardiology, Shunde Hospital of Southern Medical University, Foshan 528000, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xiaohui Huang
- Department of Cardiology, Shunde Hospital of Southern Medical University, Foshan 528000, China
| | - Weiwen Li
- Department of Cardiology, Shunde Hospital of Southern Medical University, Foshan 528000, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yunzhao Hu
- Department of Cardiology, Shunde Hospital of Southern Medical University, Foshan 528000, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
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10
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Zhai J, Luo G. GATA6‑induced FN1 activation promotes the proliferation, invasion and migration of oral squamous cell carcinoma cells. Mol Med Rep 2022; 25:102. [PMID: 35088888 PMCID: PMC8822886 DOI: 10.3892/mmr.2022.12618] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
GATA binding protein 6 (GATA6) is a transcription factor involved in cell fate decision making and tissue morphogenesis and serves a significant role in the progression of a number of types of cancer. The present study aimed to investigate the role and mechanisms underlying the effects of GATA6 in oral squamous cell carcinoma (OSCC). The expression levels of GATA6 were determined in a number of OSCC cell lines and the expression of GATA6 was knocked down to evaluate its role in the proliferation, invasion and migration of OSCC cells. Subsequently, the association between GATA6 and fibronectin 1 (FN1) was investigated using bioinformatics and further verified using dual‑luciferase reporter and chromosomal immunoprecipitation assays. Following the overexpression of FN1 in OSCC cells with GATA6 silencing, functional assays were performed to assess the mechanisms underlying GATA6 in OSCC progression. The results of the present study indicated that OSCC cells exhibited markedly upregulated expression levels of GATA6, while knockdown of GATA6 inhibited the proliferation, colony formation, invasion and migration of OSCC cells. In addition, GATA6 regulated FN1 expression levels by binding to the FN1 promoter. The suppressive effects of GATA6 knockdown on the proliferation, colony formation, invasion and migration of OSCC cells were abolished following FN1 overexpression. In conclusion, the findings of the present study demonstrated that GATA6 promoted the malignant development of OSCC cells by binding to the FN1 promotor. These results may contribute to further understanding the pathogenesis of OSCC and provide potential therapeutic targets for the clinical treatment of OSCC.
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Affiliation(s)
- Jianbo Zhai
- Welle Dental, Jingan, Shanghai 200040, P.R. China
| | - Gang Luo
- Welle Dental, Jingan, Shanghai 200040, P.R. China
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11
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Huang S, Huang P, Wu H, Wang S, Liu G. LINC02381 aggravates breast cancer through the miR-1271-5p/FN1 axis to activate PI3K/AKT pathway. Mol Carcinog 2021; 61:346-358. [PMID: 34882856 DOI: 10.1002/mc.23375] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/27/2021] [Accepted: 11/12/2021] [Indexed: 01/23/2023]
Abstract
Emerging investigations have demonstrated that lncRNAs are key crucial modulators in cancer. In this study, we investigated the role of LINC02381 in breast cancer (BC). Reverse transcriptase quantitative polymerase chain reaction measured the LINC02381 level in BC tissues and cells. Colony formation, EdU staining, wound healing and Transwell experiments examined the impact of LINC02381 depletion on BC cell phenotypes. Relationship among miR-1271-5p, LINC02381, and FN1 was tested through applying RIP, luciferase reporter, and RNA pull-down assays. We found that LINC02381 expression was elevated in BC. Functionally, LINC02381 knockdown hampered BC cell proliferation, migration, and invasion. LINC02381 overexpression accelerated tumor formation in vivo. Mechanistically, LINC02381 acted as a ceRNA to increase FN1 via decoying miR-1271-5p. Additionally, LINC02381 activated PI3K/AKT pathway by upregulating FN1. Rescue assays indicated that FN1 upregulation or PI3K/AKT activation rescued the LINC02381 knockdown-mediated inhibition on malignant phenotypes of BC cells. Overall, LINC02381 exerts carcinogenic effects in BC by the miR-1271-5p/FN1 axis to activate PI3K/AKT pathway.
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Affiliation(s)
- Shoucheng Huang
- College of Life and Health Science, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Ping Huang
- College of Chemical and Materials Engineering, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Huazhang Wu
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Bengbu, Anhui, China
| | - Song Wang
- College of Life and Health Science, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Guodong Liu
- College of Life and Health Science, Anhui Science and Technology University, Fengyang, Anhui, China
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12
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Shen Z, Chen M, Luo F, Xu H, Zhang P, Lin J, Kang M. Identification of Key Genes and Pathways Associated With Paclitaxel Resistance in Esophageal Squamous Cell Carcinoma Based on Bioinformatics Analysis. Front Genet 2021; 12:671639. [PMID: 34456964 PMCID: PMC8386171 DOI: 10.3389/fgene.2021.671639] [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: 02/24/2021] [Accepted: 07/02/2021] [Indexed: 01/07/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) ranks as the fourth leading cause of cancer-related death in China. Although paclitaxel has been shown to be effective in treating ESCC, the prolonged use of this chemical will lead to paclitaxel resistance. In order to uncover genes and pathways driving paclitaxel resistance in the progression of ESCC, bioinformatics analyses were performed based on The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database including GSE86099 and GSE161533. Differential expression analysis was performed in TCGA data and two GEO datasets to obtain differentially expressed genes (DEGs). Based on GSE161533, weighted gene co-expression network analysis (WGCNA) was conducted to identify the key modules associated with ESCC tumor status. The DEGs common to the two GEO datasets and the genes in the key modules were intersected to obtain the paclitaxel resistance-specific or non-paclitaxel resistance-specific genes, which were subjected to subsequent least absolute shrinkage and selection operator (LASSO) feature selection, whereby paclitaxel resistance-specific or non-paclitaxel resistance-specific key genes were selected. Ten machine learning models were used to validate the biological significance of these key genes; the potential therapeutic drugs for paclitaxel resistance-specific genes were also predicted. As a result, we identified 24 paclitaxel resistance-specific genes and 18 non-paclitaxel resistance-specific genes. The ESCC machine classifiers based on the key genes achieved a relatively high AUC value in the cross-validation and in an independent test set, GSE164158. A total of 207 drugs (such as bevacizumab) were predicted to be alternative therapeutics for ESCC patients with paclitaxel resistance. These results might shed light on the in-depth research of paclitaxel resistance in the context of ESCC progression.
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Affiliation(s)
- Zhimin Shen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mingduan Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Fei Luo
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Hui Xu
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Peipei Zhang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jihong Lin
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mingqiang Kang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou, China
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13
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Single Domain Antibodies as Carriers for Intracellular Drug Delivery: A Proof of Principle Study. Biomolecules 2021; 11:biom11070927. [PMID: 34206656 PMCID: PMC8301836 DOI: 10.3390/biom11070927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 12/17/2022] Open
Abstract
Antibody-drug conjugates (ADCs) are currently used for the targeted delivery of drugs to diseased cells, but intracellular drug delivery and therefore efficacy may be suboptimal because of the large size, slow internalization and ineffective intracellular trafficking of the antibody. Using a phage display method selecting internalizing phages only, we developed internalizing single domain antibodies (sdAbs) with high binding affinity to rat PDGFRβ, a receptor involved in different types of diseases. We demonstrate that these constructs have different characteristics with respect to internalization rates but all traffic to lysosomes. To compare their efficacy in targeted drug delivery, we conjugated the sdAbs to a cytotoxic drug. The conjugates showed improved cytotoxicity correlating to their internalization speed. The efficacy of the conjugates was inhibited in the presence of vacuolin-1, an inhibitor of lysosomal maturation, suggesting lysosomal trafficking is needed for efficient drug release. In conclusion, sdAb constructs with different internalization rates can be designed against the same target, and sdAbs with a high internalization rate induce more cell killing than sdAbs with a lower internalization rate in vitro. Even though the overall efficacy should also be tested in vivo, sdAbs are particularly interesting formats to be explored to obtain different internalization rates.
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14
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Fibronectin 1: A Potential Biomarker for Ovarian Cancer. DISEASE MARKERS 2021; 2021:5561651. [PMID: 34093898 PMCID: PMC8164534 DOI: 10.1155/2021/5561651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022]
Abstract
Methods OVCAR3 and A2780 are the two common cell lines that are used for ovarian cancer studies. The different invasion and migration abilities were observed by scratch tests and transwell experiments in our preliminary study. Gene chip was used to screen the expression gene in these two different cell lines, and then, the differentially expressed genes (at least 2-fold difference, P value < 0.05) were analyzed using KEGG. Result Fibronectin 1 (FN1) was found to be the most strongly correlated with the invasion and migration abilities of the OVCAR3 cells. Real-time PCR and FN1 knockout cell line was conducted and confirmed this finding. Based on the Oncomine database analysis, comparing with normal people, ovarian cancer patients exhibited high levels of FN1 expression. Additionally, higher FN1 expression was found in patients with higher FIGO stages of cancer. Conclusion FN1 could be a new biomarker for ovarian cancer detection and progress indicator.
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15
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Long J, Zhang S, Zeng X, Ouyang Y, Wang Y, Hu Z, Ye Y, Wu W, Jin F, Zhou S, Zeng Z. Development of an Immunogenomic Landscape-Based Prognostic Index of Head and Neck Squamous Cell Carcinoma. Front Mol Biosci 2020; 7:586344. [PMID: 33330624 PMCID: PMC7732611 DOI: 10.3389/fmolb.2020.586344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the eighth leading cancer by incidence worldwide, with approximately 700,000 new cases in 2018 (accounting for 11% of all cancers). The occurrence and development of tumors are closely related to the immunological function of the body and sensitivity to treatment schemes as well as prognosis. It is urgent for clinicians to systematically study patients’ immune gene maps to help select a treatment plan and analyze the potential to cure HNSCC. Here, the transcriptomic data of HNSCC samples were downloaded from The Cancer Genome Atlas (TCGA), and 4,793 genes differentially expressed in normal and cancer tissues of HNSCC were identified, including 1,182 downregulated and 3,611 upregulated genes. From these genes, 400 differentially expressed immune-related genes (IRGs) were extracted, including 95 downregulated genes and 305 upregulated genes. The prognostic values of IRGs were evaluated by univariate Cox analysis, and 236 genes that were significantly related to the overall survival (OS) of patients were identified. The signaling pathways that play roles in the prognosis of IRGs were investigated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and the expression profiles of IRGs and OS in 499 HNSCC patients based on TCGA dataset were integrated. Potential molecular mechanisms and characteristics of these HNSCC-specific IRGs were further explored with the help of a new prognostic index based on IRGs developed by least absolute shrinkage and selection operator (LASSO) Cox analysis. A total of 64 hub genes (IRGs associated with prognosis) were markedly associated with the clinical outcome of HNSCC patients. KEGG functional enrichment analysis revealed that these genes were actively involved in several pathways, e.g., cytokine–cytokine receptor interaction, T-cell receptor signaling, and natural killer cell-mediated cytotoxicity. IRG-based prognostic signatures performed moderately in prognostic predictions. Interestingly, the prognostic index based on IRGs reflected infiltration by several types of immune cells. These data screened several IRGs of clinical significance and revealed drivers of the immune repertoire, demonstrating the importance of a personalized IRG-based immune signature in the recognition, surveillance, and prognosis of HNSCC.
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Affiliation(s)
- Jinhua Long
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,School of Biology and Engineering, Guizhou Medical University, Guiyang, China.,Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, Guizhou Medical University, Guiyang, China.,Department of Head and Neck Oncology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shichao Zhang
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,School of Biology and Engineering, Guizhou Medical University, Guiyang, China.,Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, Guizhou Medical University, Guiyang, China.,Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Xianlin Zeng
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,School of Biology and Engineering, Guizhou Medical University, Guiyang, China.,Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, Guizhou Medical University, Guiyang, China.,Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Yan Ouyang
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Yun Wang
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,School of Biology and Engineering, Guizhou Medical University, Guiyang, China.,Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, Guizhou Medical University, Guiyang, China.,Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Zuquan Hu
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,School of Biology and Engineering, Guizhou Medical University, Guiyang, China.,Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, Guizhou Medical University, Guiyang, China.,Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Yuannong Ye
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,School of Biology and Engineering, Guizhou Medical University, Guiyang, China.,Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Weili Wu
- Department of Head and Neck Oncology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Feng Jin
- Department of Head and Neck Oncology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shi Zhou
- Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zhu Zeng
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,School of Biology and Engineering, Guizhou Medical University, Guiyang, China.,Key Laboratory of Infectious Immune and Antibody Engineering in Guizhou Province, Guizhou Medical University, Guiyang, China.,Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
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16
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Hu C, Chen X, Yao C, Liu Y, Xu H, Zhou G, Xia H, Xia J. Body mass index-associated molecular characteristics involved in tumor immune and metabolic pathways. Cancer Metab 2020; 8:21. [PMID: 32999719 PMCID: PMC7517824 DOI: 10.1186/s40170-020-00225-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
Background Overweight or obesity has been evidenced as an important risk factor involved in the incidence, mortality, and therapy response of multiple malignancies. However, the differences between healthy and obesity tumor patients at the molecular and multi-omics levels remain unclear. Methods Our study performed a comprehensive and multidimensional analysis in fourteen tumor types of The Cancer Genome Atlas (TCGA) and found body mass index (BMI)-related genes in multiple tumor types. Furthermore, we compared composite expression between normal, overweight, and obese patients of each immune cell subpopulation and metabolism gene subset. Statistical significance was calculated via the Kruskal-Wallis rank-sum test. Results Our analysis revealed that BMI-related genes are enriched in multiple tumor-related biological pathways involved in intracellular signaling, immune response, and metabolism. We also found the different relationships between BMI and different immune cell infiltration and metabolic pathway activity. Importantly, we found that many clinically actionable genes were BMI-affect genes. Conclusion Overall, our data indicated that BMI-associated molecular characteristics involved in tumor immune and metabolic pathways, which may highlight the clinical importance of considering BMI-associated molecular signatures in cancer precision medicine.
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Affiliation(s)
- Chao Hu
- Department of Pathology in the School of Basic Medical Sciences & The Affiliated Sir Run Run Hospital & State Key Laboratory of Reproductive Medicine & Key Laboratory of Antibody Technique of National Health Commission, Nanjing Medical University, Nanjing 211166, China
| | - Xiong Chen
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Chengyun Yao
- Department of Pathology in the School of Basic Medical Sciences & The Affiliated Sir Run Run Hospital & State Key Laboratory of Reproductive Medicine & Key Laboratory of Antibody Technique of National Health Commission, Nanjing Medical University, Nanjing 211166, China.,The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Yu Liu
- Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Haojun Xu
- Department of Pathology in the School of Basic Medical Sciences & The Affiliated Sir Run Run Hospital & State Key Laboratory of Reproductive Medicine & Key Laboratory of Antibody Technique of National Health Commission, Nanjing Medical University, Nanjing 211166, China
| | - Guoren Zhou
- The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Hongping Xia
- Department of Pathology in the School of Basic Medical Sciences & The Affiliated Sir Run Run Hospital & State Key Laboratory of Reproductive Medicine & Key Laboratory of Antibody Technique of National Health Commission, Nanjing Medical University, Nanjing 211166, China.,The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.,The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China.,Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Jinglin Xia
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
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17
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Identification of Potential Biomarkers for Thyroid Cancer Using Bioinformatics Strategy: A Study Based on GEO Datasets. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9710421. [PMID: 32337286 PMCID: PMC7152968 DOI: 10.1155/2020/9710421] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/29/2020] [Accepted: 03/05/2020] [Indexed: 12/13/2022]
Abstract
Background The molecular mechanisms and genetic markers of thyroid cancer are unclear. In this study, we used bioinformatics to screen for key genes and pathways associated with thyroid cancer development and to reveal its potential molecular mechanisms. Methods The GSE3467, GSE3678, GSE33630, and GSE53157 expression profiles downloaded from the Gene Expression Omnibus database (GEO) contained a total of 164 tissue samples (64 normal thyroid tissue samples and 100 thyroid cancer samples). The four datasets were integrated and analyzed by the RobustRankAggreg (RRA) method to obtain differentially expressed genes (DEGs). Using these DEGs, we performed gene ontology (GO) functional annotation, pathway analysis, protein-protein interaction (PPI) analysis and survival analysis. Then, CMap was used to identify the candidate small molecules that might reverse thyroid cancer gene expression. Results By integrating the four datasets, 330 DEGs, including 154 upregulated and 176 downregulated genes, were identified. GO analysis showed that the upregulated genes were mainly involved in extracellular region, extracellular exosome, and heparin binding. The downregulated genes were mainly concentrated in thyroid hormone generation and proteinaceous extracellular matrix. Pathway analysis showed that the upregulated DEGs were mainly attached to ECM-receptor interaction, p53 signaling pathway, and TGF-beta signaling pathway. Downregulation of DEGs was mainly involved in tyrosine metabolism, mineral absorption, and thyroxine biosynthesis. Among the top 30 hub genes obtained in PPI network, the expression levels of FN1, NMU, CHRDL1, GNAI1, ITGA2, GNA14 and AVPR1A were associated with the prognosis of thyroid cancer. Finally, four small molecules that could reverse the gene expression induced by thyroid cancer, namely ikarugamycin, adrenosterone, hexamethonium bromide and clofazimine, were obtained in the CMap database. Conclusion The identification of the key genes and pathways enhances the understanding of the molecular mechanisms for thyroid cancer. In addition, these key genes may be potential therapeutic targets and biomarkers for the treatment of thyroid cancer.
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Li M, Wang K, Pang Y, Zhang H, Peng H, Shi Q, Zhang Z, Cui X, Li F. Secreted Phosphoprotein 1 (SPP1) and Fibronectin 1 (FN1) Are Associated with Progression and Prognosis of Esophageal Cancer as Identified by Integrated Expression Profiles Analysis. Med Sci Monit 2020; 26:e920355. [PMID: 32208405 PMCID: PMC7111131 DOI: 10.12659/msm.920355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Esophageal cancer is a malignant tumor with a complex pathogenesis and a poor 5-year survival rate, which encourages researchers to explore its molecular mechanisms deeper to improve the prognosis. Material/Methods DEGs were from 4 Gene Expression Omnibus (GEO) databases (GSE92396, GSE20347, GSE23400, and GSE45168) including 87 esophageal tumor samples and 84 normal samples. We performed Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Protein-Protein interaction (PPI) analysis, and GeneMANIA to identify the DEGs. Gene set enrichment analysis (GSEA) and Kaplan-Meier survival analyses were performed. Results There was an overlapping subset consisting of 120 DEGs that was present in all esophageal tumor samples. The DEGs were enriched in extracellular matrix (ECM)-receptor interaction, as well as focal adhesion and transcriptional mis-regulation in cancer. The 2 most crucial regulatory pathways in esophageal cancer were the amebiasis pathway and the PI3K-Akt signaling pathway. Secreted phosphoprotein 1 (SPP1) and fibronectin 1 (FN1) were selected and verified in an independent cohort and samples using the TCGA and GTEx projects. Gene set enrichment analysis (GSEA) showed that proteasome and nucleotide excision repair were 2 most differentially enriched pathways in the SPP1 high-expression phenotype, and ECM-receptor interaction and focal adhesion in FN1 high-expression phenotype. Kaplan-Meier survival analysis showed that SPP1 and FN1 were significantly positively related to overall survival and had the potential to predict patient relapse. Conclusions Our analysis is the first to show that SPP1 and FN1 might work as biological markers of progression and prognosis in esophageal carcinoma (ESCA).
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Affiliation(s)
- Menglu Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China (mainland)
| | - Kaige Wang
- Department of Pathology and Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China (mainland)
| | - Yanhua Pang
- Department of Gastroenterology, Beijing Chaoyang Hospital, Beijing, China (mainland)
| | - Hongpan Zhang
- Department of Pathology and Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China (mainland)
| | - Hao Peng
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China (mainland)
| | - Qi Shi
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China (mainland)
| | - Zhiyu Zhang
- Department of Pathology and Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China (mainland)
| | - Xiaobin Cui
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China (mainland)
| | - Feng Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China (mainland).,Department of Pathology and Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China (mainland)
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Narwade N, Patel S, Alam A, Chattopadhyay S, Mittal S, Kulkarni A. Mapping of scaffold/matrix attachment regions in human genome: a data mining exercise. Nucleic Acids Res 2019; 47:7247-7261. [PMID: 31265077 PMCID: PMC6698742 DOI: 10.1093/nar/gkz562] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/08/2019] [Accepted: 06/27/2019] [Indexed: 11/14/2022] Open
Abstract
Scaffold/matrix attachment regions (S/MARs) are DNA elements that serve to compartmentalize the chromatin into structural and functional domains. These elements are involved in control of gene expression which governs the phenotype and also plays role in disease biology. Therefore, genome-wide understanding of these elements holds great therapeutic promise. Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. However, a comprehensive genome-wide map of human S/MARs is yet not available. Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. Along with co-ordinate (location) details of S/MARs, the dataset also revealed details of S/MAR features, namely, length, inter-SMAR length (the chromatin loop size), nucleotide repeats, motif abundance, chromosomal distribution and genomic context. S/MARs identified in present study and their subsequent analysis also suggests that these elements act as hotspots for integration of retroviruses. Therefore, these data will help toward better understanding of genome functioning and designing effective anti-viral therapeutics. In order to facilitate user friendly browsing and retrieval of the data obtained in present study, a web interface, MARome (http://bioinfo.net.in/MARome), has been developed.
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Affiliation(s)
- Nitin Narwade
- Bioinformatics Centre, Savitribai Phule Pune University, Pune - 411 007, Maharashtra, India
| | - Sonal Patel
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Pune - 411 007, Maharashtra, India
| | - Aftab Alam
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Pune - 411 007, Maharashtra, India
| | - Samit Chattopadhyay
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Pune - 411 007, Maharashtra, India.,Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata - 700 032, West Bengal, India
| | - Smriti Mittal
- Department of Biotechnology, Savitribai Phule Pune University, Pune - 411 007, Maharashtra, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune - 411 007, Maharashtra, India
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Glatzel-Plucińska N, Piotrowska A, Dzięgiel P, Podhorska-Okołów M. The Role of SATB1 in Tumour Progression and Metastasis. Int J Mol Sci 2019; 20:E4156. [PMID: 31450715 PMCID: PMC6747166 DOI: 10.3390/ijms20174156] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/16/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022] Open
Abstract
Carcinogenesis is a long-drawn, multistep process, in which metastatic spread is an unequivocal hallmark of a poor prognosis. The progression and dissemination of epithelial cancers is commonly thought to rely on the epidermal-mesenchymal transition (EMT) process. During EMT, epithelial cells lose their junctions and apical-basal polarity, and they acquire a mesenchymal phenotype with its migratory and invasive capabilities. One of the proteins involved in cancer progression and EMT may be SATB1 (Special AT-Rich Binding Protein 1)-a chromatin organiser and a global transcriptional regulator. SATB1 organizes chromatin into spatial loops, providing a "docking site" necessary for the binding of further transcription factors and chromatin modifying enzymes. SATB1 has the ability to regulate whole sets of genes, even those located on distant chromosomes. SATB1 was found to be overexpressed in numerous malignancies, including lymphomas, breast, colorectal, prostate, liver, bladder and ovarian cancers. In the solid tumours, an elevated SATB1 level was observed to be associated with an aggressive phenotype, presence of lymph node, distant metastases, and a poor prognosis. In this review, we briefly describe the prognostic significance of SATB1 expression in most common human cancers, and analyse its impact on EMT and metastasis.
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Affiliation(s)
- Natalia Glatzel-Plucińska
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland.
| | - Aleksandra Piotrowska
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
- Department of Physiotherapy, Wroclaw University School of Physical Education, 51-612 Wroclaw, Poland
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21
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Qadir F, Lalli A, Dar HH, Hwang S, Aldehlawi H, Ma H, Dai H, Waseem A, Teh MT. Clinical correlation of opposing molecular signatures in head and neck squamous cell carcinoma. BMC Cancer 2019; 19:830. [PMID: 31443700 PMCID: PMC6708230 DOI: 10.1186/s12885-019-6059-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background The concept of head and neck cancers (HNSCC) having unique molecular signatures is well accepted but relating this to clinical presentation and disease behaviour is essential for patient benefit. Currently the clinical significance of HNSCC molecular subtypes is uncertain therefore personalisation of HNSCC treatment is not yet possible. Methods We performed meta-analysis on 8 microarray studies and identified six significantly up- (PLAU, FN1, CDCA5) and down-regulated (CRNN, CLEC3B and DUOX1) genes which were subsequently quantified by RT-qPCR in 100 HNSCC patient margin and core tumour samples. Results Retrospective correlation with sociodemographic and clinicopathological patient details identified two subgroups of opposing molecular signature (+q6 and -q6) that correlated to two recognised high-risk HNSCC populations in the UK. The +q6 group were older, male, and excessive alcohol users whilst the –q6 group were younger, female, paan-chewers and predominantly Bangladeshi. Additionally, all patients with tumour recurrence were in the latter subgroup. Conclusions We provide the first evidence linking distinct molecular signatures in HNSCC with clinical presentations. Prospective trials are required to determine the correlation between these distinct genotypes and disease progression or treatment response. This is an important step towards the ultimate goal of improving outcomes by utilising personalised molecular-signature-guided treatments for HNSCC patients.
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Affiliation(s)
- Fatima Qadir
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Anand Lalli
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Huma Habib Dar
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Sungjae Hwang
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Hebah Aldehlawi
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Hong Ma
- China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Stomatological Hospital of Guizhou Medical University, Guizhou, China
| | - Haiyan Dai
- China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Stomatological Hospital of Guizhou Medical University, Guizhou, China
| | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Muy-Teck Teh
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK. .,China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Stomatological Hospital of Guizhou Medical University, Guizhou, China. .,Cancer Research Institute, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.
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22
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Xu J, Lv H, Zhang B, Xu F, Zhu H, Chen B, Zhu C, Shen J. miR-30b-5p acts as a tumor suppressor microRNA in esophageal squamous cell carcinoma. J Thorac Dis 2019; 11:3015-3029. [PMID: 31463131 DOI: 10.21037/jtd.2019.07.50] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background To study miR-30b-5p expression in esophageal squamous cell carcinoma (ESCC) by comparisons between tumor tissues and matched adjacent non-cancerous tissues to elucidate the correlation between miR-30b-5p expression and ESCC clinical parameters, and to explore the signaling pathways associated with miR-30b-5p and key target genes. Methods Clinical data, cancer tissues, and adjacent non-cancerous tissues of 32 patients diagnosed with ESCC were collected from Taizhou Hospital of Zhejiang Province. The expression levels of miR-30b-5p were determined by real-time polymerase chain reaction (RT-PCR). mRNA data for ESCC tissues and normal tissues, and clinical materials of patients with ESCC were obtained from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA). Associations between miR-30b-5p expression and clinical features of patients with ESCC and overall survival were explored. A bioinformatics analysis was performed to determine the pathways and key miR-30b-5p targets associated with ESCC. Additionally, a cytological experiment was performed to evaluate the biological functions of miR-30b-5p. Finally, correlations between miR-30b-5p and key targets involved in PI3K/Akt signaling pathways were validated by western blotting. Results The expression level of miR-30b-5p in the 32 ESCC tissues was significantly lower than that in adjacent normal tissues (P<0.01) and was significantly disparate in the T stage, with higher expression in T1 than in T2 (P<0.05). Among the patients with higher expression levels of miR-30b-5p in ESCC tissues than in adjacent normal tissues, patients with higher expression of miR-30b-5p had a better prognosis (P<0.05). An analysis of gene chip data from the GEO database showed similar results. A gene enrichment analysis indicated a series of pathways that may be associated with the downregulation of miR-30b-5p, including focal adhesion, ECM-receptor interaction, and PI3K/Akt signaling pathways. Seven key target genes (PDGFRB, VIM, ITGA5, ACTN1, THBS2, SERPINE1, and RUNX2) were identified; these were found to be upregulated in ESCC tissues and were negatively correlated with miR-30b-5p. Functional experiments showed that miR-30b-5p attenuated migration (P<0.01) and invasion (P<0.05) in the Eca109 cell line. Moreover, the levels of ITGA5, PDGFRB, p-PI3K, and p-AKT, which are involved in the PI3K/Akt signaling pathway, were decreased in the miR-30b-5p-overexpressing Eca109 cell line. Conclusions Upregulated miR-30b-5p may inhibit migration and invasion in ESCC by targeting ITGA5, PDGFRB, and signaling pathways, such as PI3K/Akt, involved in ESCC regulation. Our results indicate that miR-30b-5p plays an important role in the occurrence and progression of ESCC and is a potential therapeutic target.
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Affiliation(s)
- Jianfeng Xu
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou 317000, China
| | - Haiyan Lv
- Enze Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou 317000, China
| | - Bo Zhang
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou 317000, China
| | - Feng Xu
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou 317000, China
| | - Hongyu Zhu
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou 317000, China
| | - Baofu Chen
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou 317000, China
| | - Chengchu Zhu
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou 317000, China
| | - Jianfei Shen
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou 317000, China
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23
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Zhou Y, Shu C, Huang Y. Fibronectin promotes cervical cancer tumorigenesis through activating FAK signaling pathway. J Cell Biochem 2019; 120:10988-10997. [PMID: 30977220 DOI: 10.1002/jcb.28282] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/24/2018] [Indexed: 01/24/2023]
Abstract
Cervical cancer is a cancer arising from the cervix, and it is the fourth most common cause of death in women. Overexpression of fibronectin 1 (FN1) was observed in many tumors and associated with the survival and metastasis of cancer cells. However, the mechanism by which FN1 promotes cervical cancer cell viability, migration, adhesion, and invasion, and inhibits cell apoptosis through focal adhesion kinase (FAK) signaling pathway remains to be investigated. Our results demonstrated that FN1 was upregulated in patients with cervical cancer and higher FN1 expression correlated with a poor prognosis for patients with cervical cancer. FN1 knockdown by small interfering RNA (siRNA) inhibited SiHa cell viability, migration, invasion, and adhesion, and promoted cell apoptosis. FN1 overexpression in CaSki cell promoted cell viability, migration, invasion, and adhesion, and inhibited cell apoptosis. Further, phosphorylation of FAK, a main downstream signaling molecule of FN1, and the protein expression of Bcl-2/Bax, matrix metalloproteinase 2 (MMP-2), matrix metalloproteinase 9 (MMP-9), and N-cadherin was upregulated in CaSki cells with FN1 overexpression, but caspase-3 protein expression was downregulated. The FAK phosphorylation inhibitor PF573228 inhibited FN1 overexpression-induced expression of those proteins in CaSki cells with FN1 overexpression. In vivo experiment demonstrated that FN1 knockdown significantly inhibited FN1 expression, phosphorylation of FAK, and tumor growth in xenograft from the nude mice. These results suggest that FN1 regulates the viability, apoptosis, migration, invasion, and adhesion of cervical cancer cells through the FAK signaling pathway and is a potential therapeutic target in the treatment of cervical cancer.
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Affiliation(s)
- Yuzhen Zhou
- Department of Obstetrics and Gynecology, Suzhou Traditional Chinese and Western Medicine Hospital, Suzhou, China
| | - Changzhen Shu
- Department of Obstetrics and Gynecology, Suzhou Traditional Chinese and Western Medicine Hospital, Suzhou, China
| | - Yan Huang
- Department of Obstetrics and Gynecology, Suzhou Traditional Chinese and Western Medicine Hospital, Suzhou, China
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24
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Ma J, Xiao Y, Tian B, Chen S, Zhang B, Wu J, Wu Z, Li X, Tang J, Yang D, Zhou Y, Wang H, Su M, Wang W. Genome-wide analyses of long non-coding RNA expression profiles and functional network analysis in esophageal squamous cell carcinoma. Sci Rep 2019; 9:9162. [PMID: 31235759 PMCID: PMC6591223 DOI: 10.1038/s41598-019-45493-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 06/07/2019] [Indexed: 12/15/2022] Open
Abstract
Esophageal cancer (EC) is a serious malignancy and that is the fifth leading cause of cancer-related death worldwide. Esophageal squamous cell carcinoma (ESCC) is the main subtype of EC in China. In recent years, long non-coding RNAs (lncRNAs) have demonstrated to be novel tumor-associated regulatory factors. However, the functions and mechanisms of lncRNAs in ESCC have not been fully understood. In this study, we attempted to construct Genome-wide expression profiles of lncRNAs and their potential functions in ESCC. By using microarray, we found a total of 2,366 lncRNAs (1,032 upregulated and 1,334 downregulated) and 3,052 mRNAs (1,477 upregulated and 1,575 downregulated) were differentially expressed between the paired five ESCC tumor tissues and adjacent normal esophageal tissues (fold change, FC ≥2.0 or ≤0.5, p ≤ 0.05). Eight lncRNAs were detected by qRT-PCR to verify the results of the microarray, and the clinicopathological parameters were analyzed in 53 patients with ESCC. GO analysis and KEGG pathway analysis showed that the main biological functions of these abnormal lncRNAs were related to immune response, extracellular vesicular exosome, and protein binding. At the same time, the cis and trans models were used to analyze the potential synergistic regulatory relationship between lncRNAs and their potential target genes. Related genes were the processes that affect cell growth, differentiation, and migration. Then we mapped the lncRNAs-mRNAs co-expression pattern by calculating the PCCs of each lncRNA and mRNA expression value. Furthermore, we investigated the function and potential mechanism of a novel highly expressed lncRNA, lnc-KIAA1244-2, and found that its expression is associated with tumor size, N classification and clinical stage. Knockdown of lnc-KIAA1244-2 inhibited the cell proliferation and inhibited the TNFAIP3 expression in Eca-109 cells. Taken together, the expression patterns of lncRNAs and mRNAs in ESCC tumor tissues are different from those in normal adjacent tissues, and some abnormal expressed lncRNAs may play important roles in the development and progression of ESCC. Lnc-KIAA1244-2 could promote the cell proliferation of ESCC cells and might be a potent therapeutic target for ESCC.
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Affiliation(s)
- Junliang Ma
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China.,Hunan University of Medicine, Huaihua, Hunan, 418000, P.R. China
| | - Yuhang Xiao
- Department of Pharmacy, Xiangya Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410001, P.R. China
| | - Bo Tian
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China
| | - Shaolin Chen
- Hunan University of Medicine, Huaihua, Hunan, 418000, P.R. China
| | - Baihua Zhang
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China
| | - Jie Wu
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China
| | - Zhining Wu
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China
| | - Xu Li
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China
| | - Jinming Tang
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China
| | - Desong Yang
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China
| | - Yong Zhou
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China
| | - Hui Wang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China
| | - Min Su
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China. .,Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China.
| | - Wenxiang Wang
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China. .,Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P.R. China.
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25
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Regan-Fendt KE, Xu J, DiVincenzo M, Duggan MC, Shakya R, Na R, Carson WE, Payne PRO, Li F. Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes. NPJ Syst Biol Appl 2019; 5:6. [PMID: 30820351 PMCID: PMC6391384 DOI: 10.1038/s41540-019-0085-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 01/23/2019] [Indexed: 12/31/2022] Open
Abstract
Systems biology perspectives are crucial for understanding the pathophysiology of complex diseases, and therefore hold great promise for the discovery of novel treatment strategies. Drug combinations have been shown to improve durability and reduce resistance to available first-line therapies in a variety of cancers; however, traditional drug discovery approaches are prohibitively cost and labor-intensive to evaluate large-scale matrices of potential drug combinations. Computational methods are needed to efficiently model complex interactions of drug target pathways and identify mechanisms underlying drug combination synergy. In this study, we employ a computational approach, SynGeNet (Synergy from Gene expression and Network mining), which integrates transcriptomics-based connectivity mapping and network centrality analysis to analyze disease networks and predict drug combinations. As an exemplar of a disease in which combination therapies demonstrate efficacy in genomic-specific contexts, we investigate malignant melanoma. We employed SynGeNet to generate drug combination predictions for each of the four major genomic subtypes of melanoma (BRAF, NRAS, NF1, and triple wild type) using publicly available gene expression and mutation data. We validated synergistic drug combinations predicted by our method across all genomic subtypes using results from a high-throughput drug screening study across. Finally, we prospectively validated the drug combination for BRAF-mutant melanoma that was top ranked by our approach, vemurafenib (BRAF inhibitor) + tretinoin (retinoic acid receptor agonist), using both in vitro and in vivo models of BRAF-mutant melanoma and RNA-sequencing analysis of drug-treated melanoma cells to validate the predicted mechanisms. Our approach is applicable to a wide range of disease domains, and, importantly, can model disease-relevant protein subnetworks in precision medicine contexts.
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Affiliation(s)
- Kelly E Regan-Fendt
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Jielin Xu
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Mallory DiVincenzo
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Megan C Duggan
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Reena Shakya
- Target Validation Shared Resource, The Ohio State University, Columbus, OH, USA
| | - Ryejung Na
- Target Validation Shared Resource, The Ohio State University, Columbus, OH, USA
| | - William E Carson
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Philip R O Payne
- Institute for Informatics, Washington University in St. Louis, St. Louis, MO, USA
| | - Fuhai Li
- Institute for Informatics, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA.
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26
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Zhao L, Zheng Y, Ji Y, Zhang X. The expression of special AT-rich binding protein 1 in cervical cancer and its clinical significance. Onco Targets Ther 2019; 12:945-951. [PMID: 30774380 PMCID: PMC6361226 DOI: 10.2147/ott.s191414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background The oncogenic potential of special AT-rich binding protein 1 (SATB1) has been reported in various types of cancer, but its function in cervical cancer remains not fully investigated. This study aimed to investigate the effect of SATB1 mRNA expression on tumor progression and outcomes in the cervical cancer patients. Methods A total of 33 cervical cancer patients treated in our hospital from September 2012 to December 2015 were included. The mRNA expression level of STAB1 in cervical cancer tissue was determined by real-time PCR, and the patients were divided into dichotomous groups based on their SATB1 expression level. Clinical characteristics, recurrence, and survival outcomes were compared between groups. Results Compared with the SATB1-low group, the SATB1-high group had significantly advanced International Federation of Gynecology and Obstetrics (FIGO) stages (P=0.037) and histologic grade (P=0.036). Kaplan–Meier analysis showed that SATB1-high group had a worse overall survival (P=0.078, marginal significant). In the subgroup analysis of pathological types, adenocarcinomas group (n=8) had a significantly higher SATB1 expression level as compared with the squamous cell carcinomas (n=18) and adenosquamous carcinomas (n=7) groups (both P<0.05). Cervical squamous cell carcinomas patients with a high-expression SATB1 (n=8) had more advanced FIGO stages (P=0.015) and histologic grades (P=0.060, marginal significant) as well as a higher (P=0.069, marginal significant) incidence of lymphatic metastasis than those with a low expression of SATB1 (n=10). Conclusion These results showed that expression of SATB1 may have an effect on the disease progression and survival outcome of cervical cancer.
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Affiliation(s)
- Lijie Zhao
- Department of Gynecology, Maternal and Child Health Hospital of Foshan, Foshan 528000, Guangdong, China,
| | - Yuhua Zheng
- Department of Gynecology, Maternal and Child Health Hospital of Foshan, Foshan 528000, Guangdong, China,
| | - Yong Ji
- Department of Surgery, The First People's Hospital of Foshan, Foshan 528000, Guangdong, China,
| | - Xiaoying Zhang
- Department of Gynecology, Jiashi County People's Hospital of Kashi Region, Kashi, Xinjiang 844000, China
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27
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SATB family chromatin organizers as master regulators of tumor progression. Oncogene 2018; 38:1989-2004. [PMID: 30413763 DOI: 10.1038/s41388-018-0541-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/30/2018] [Accepted: 09/02/2018] [Indexed: 02/07/2023]
Abstract
SATB (Special AT-rich binding protein) family proteins have emerged as key regulators that integrate higher-order chromatin organization with the regulation of gene expression. Studies over the past decade have elucidated the specific roles of SATB1 and SATB2, two closely related members of this family, in cancer progression. SATB family chromatin organizers play diverse and important roles in regulating the dynamic equilibrium of apoptosis, cell invasion, metastasis, proliferation, angiogenesis, and immune modulation. This review highlights cellular and molecular events governed by SATB1 influencing the structural organization of chromatin and interacting with several co-activators and co-repressors of transcription towards tumor progression. SATB1 expression across tumor cell types generates cellular and molecular heterogeneity culminating in tumor relapse and metastasis. SATB1 exhibits dynamic expression within intratumoral cell types regulated by the tumor microenvironment, which culminates towards tumor progression. Recent studies suggested that cell-specific expression of SATB1 across tumor recruited dendritic cells (DC), cytotoxic T lymphocytes (CTL), T regulatory cells (Tregs) and tumor epithelial cells along with tumor microenvironment act as primary determinants of tumor progression and tumor inflammation. In contrast, SATB2 is differentially expressed in an array of cancer types and is involved in tumorigenesis. Survival analysis for patients across an array of cancer types correlated with expression of SATB family chromatin organizers suggested tissue-specific expression of SATB1 and SATB2 contributing to disease prognosis. In this context, it is pertinent to understand molecular players, cellular pathways, genetic and epigenetic mechanisms governed by cell types within tumors regulated by SATB proteins. We propose that patient survival analysis based on the expression profile of SATB chromatin organizers would facilitate their unequivocal establishment as prognostic markers and therapeutic targets for cancer therapy.
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28
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Functional relevance of SATB1 in immune regulation and tumorigenesis. Biomed Pharmacother 2018; 104:87-93. [DOI: 10.1016/j.biopha.2018.05.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/05/2018] [Accepted: 05/08/2018] [Indexed: 02/07/2023] Open
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29
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Li L, Yue GGL, Lee JKM, Wong ECW, Fung KP, Yu J, Lau CBS, Chiu PWY. Gene expression profiling reveals the plausible mechanisms underlying the antitumor and antimetastasis effects of Andrographis paniculata in esophageal cancer. Phytother Res 2018; 32:1388-1396. [PMID: 29577460 DOI: 10.1002/ptr.6074] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 02/12/2018] [Indexed: 12/28/2022]
Abstract
Esophageal cancer (EC) is a seriously invasive malignancy with high mortality and poor prognosis. Metastasis of EC is the major cause of mortality. Our studies previously demonstrated that a herbal medicine Andrographis paniculata (AP) significantly suppressed EC growth and metastasis in vitro and in vivo. However, the underlying mechanisms responsible for these effects have not yet been systematically elucidated. In this context, gene expression profiling of AP-treated squamous EC cells (EC-109) was performed to reveal the regulatory mechanisms of AP in antitumor and antimetastasis signaling pathways using gene expression microarray analysis. Differentially expressed genes were identified by Affymetrix Gene Chip, followed by the real-time polymerase chain reaction validation. The results showed that the canonical pathways were significantly regulated by AP treatment, including multiple genes related to proliferation, apoptosis, intercellular adhesion, metastatic processes, and drug resistance, such as WNT, TGF-β, MAPK and ErbB signaling pathways, and ATP-binding cassette transporter subfamily members. This genomic study emerges candidate molecular targets and pathways to reveal the mechanisms involved in AP's effects, which provides scientific evidence to support the clinical application of AP in EC treatment.
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Affiliation(s)
- Lin Li
- Department of Surgery, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
| | - Grace Gar-Lee Yue
- Institute of Chinese Medicine and State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK), Shatin, New Territories, Hong Kong
| | - Julia Kin-Ming Lee
- Institute of Chinese Medicine and State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK), Shatin, New Territories, Hong Kong
| | - Eric Chun-Wai Wong
- Institute of Chinese Medicine and State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK), Shatin, New Territories, Hong Kong
| | - Kwok-Pui Fung
- Institute of Chinese Medicine and State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK), Shatin, New Territories, Hong Kong.,School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Jun Yu
- Department of Medicine and Therapeutics and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Clara Bik-San Lau
- Institute of Chinese Medicine and State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK), Shatin, New Territories, Hong Kong
| | - Philip Wai-Yan Chiu
- Department of Surgery, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
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30
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Feng Y, Wang X, Wang Q. Expression of SATB1 and E-cad in tissues of patients with endometrial carcinoma and the relationship with clinicopathological features. Exp Ther Med 2018; 15:4339-4343. [PMID: 29725375 PMCID: PMC5920497 DOI: 10.3892/etm.2018.5954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/12/2017] [Indexed: 12/29/2022] Open
Abstract
The expression of special AT-rich sequence binding protein 1 (SATB1) and E-cadherin (E-cad) in tissues of patients with endometrial carcinoma and the relationships with clinicopathological features were investigated. One hundred and four cases of carcinoma tissues and 104 cases of para-carcinoma tissues of patients pathologically diagnosed as endometrial carcinoma in Affiliated Hospital of Jining Medical University (Jining, China) from August 2015 to August 2016 were selected. The expressions of SATB1 and E-cad in tissues was detected via streptavidin peroxidase biotin (SP) immunohistochemical method, and the relationship with clinicopathological features of patients was analyzed. SATB1 was positively expressed in 71 out of 104 cases of endometrial carcinoma tissues (the expression rate was 68.27%) and in 25 out of 104 cases of para-carcinoma tissues (the expression rate was 24.03%). The expression of SATB1 in endometrial carcinoma tissues was significantly higher than that in para-carcinoma tissues (P<0.05). E-cad was positively expressed in 60 out of 104 cases of carcinoma tissues (the expression rate was 57.6%) and 95 out of 104 cases of para-carcinoma tissues (the positive expression rate was 91.3%) (P<0.05). The expression of SATB1 and E-cad in endometrial carcinoma tissues was not associated with the menopausal status or age of patients (P>0.05), but correlated with the histological grade of endometrial carcinoma, depth of tumor invasion, lymph node metastasis and tumor lymph node metastasis (TNM) staging (P<0.05). In conclusion, SATB1 and E-cad play important roles in the occurrence and development of endometrial carcinoma, which are of great significance to the potential therapeutic target and prognosis estimation of endometrial carcinoma.
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Affiliation(s)
- Yanli Feng
- Department of Gynecology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Xin Wang
- Jining Hospital of Traditional Chinese Medicine, Jining, Shandong 272029, P.R. China
| | - Quanyi Wang
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
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31
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The Special AT-rich Sequence Binding Protein 1 (SATB1) and its role in solid tumors. Cancer Lett 2018; 417:96-111. [DOI: 10.1016/j.canlet.2017.12.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 02/07/2023]
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32
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Wang Y, Pan T, Li L, Wang H, Li J, Zhang D, Yang H. Knockdown of TGIF attenuates the proliferation and tumorigenicity of EC109 cells and promotes cisplatin-induced apoptosis. Oncol Lett 2017; 14:6519-6524. [PMID: 29344116 PMCID: PMC5754828 DOI: 10.3892/ol.2017.7009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/07/2017] [Indexed: 12/23/2022] Open
Abstract
A previous study has reported that frequent amplifications of the TG-interacting factor (TGIF) were observed in esophageal squamous cell carcinoma. The aim of the present study was to investigate the potential role of TGIF in the proliferation and tumorigenicity of the esophageal cancer cell line EC109 and cisplatin-induced apoptosis. Stable TGIF-knockdown EC109 cell line was established by infecting short hairpin RNA (shRNA) lentiviral particles. Soft agar and tumor xenograft assays were applied in nude mice. Flow cytometry was employed to evaluate the cell cycle and apoptosis. Western blot analysis was used to detect the expression of proteins. TGIF knockdown suppressed EC109 cell proliferation, colony formation in soft agar and tumor growth in nude mice, induced cell cycle arrest in the G1 phase, and promoted cisplatin-induced apoptosis. In addition, TGIF knockdown significantly reduced the expression of phospho-Rb in EC109 cells. The reduced level of full length PARP expression and the increased level of cleaved caspase-3 expression were observed in EC109 cells with the treatment of cisplatin and TGIF knockdown. The results suggest that knockdown of TGIF attenuated the proliferation and tumorigenicity of EC109 cells, and promoted cisplatin-induced apoptosis.
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Affiliation(s)
- Yadong Wang
- Department of Toxicology, Henan Center for Disease Control and Prevention, Zhengzhou, Henan 450016, P.R. China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Teng Pan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Li Li
- Department of Toxicology, Henan Center for Disease Control and Prevention, Zhengzhou, Henan 450016, P.R. China
| | - Haiyu Wang
- Department of Toxicology, Henan Center for Disease Control and Prevention, Zhengzhou, Henan 450016, P.R. China
| | - Jiangmin Li
- Department of Toxicology, Henan Center for Disease Control and Prevention, Zhengzhou, Henan 450016, P.R. China
| | - Ding Zhang
- Department of Toxicology, Henan Center for Disease Control and Prevention, Zhengzhou, Henan 450016, P.R. China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
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33
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Wang X, Yu X, Wang Q, Lu Y, Chen H. Expression and clinical significance of SATB1 and TLR4 in breast cancer. Oncol Lett 2017; 14:3611-3615. [PMID: 28927120 PMCID: PMC5587979 DOI: 10.3892/ol.2017.6571] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/04/2017] [Indexed: 12/11/2022] Open
Abstract
This study investigated the expression of special AT-rich sequence-binding protein 1 (SATB1) and toll-like receptor 4 (TLR4) protein in breast cancer and its clinical significance. We collected breast cancer tissues from 120 patients and adjacent non-cancerous tissue from 53 patients. SATB1 was expressed in 89 cases of breast cancer (74.17%) and in 7 cases of adjacent non-cancerous tissue (13.21%). TLR4 was expressed in 70 cases of breast cancer tissues (58.33%) and in 48 cases of adjacent non-cancerous tissue (90.57%). The differences of SATB and TLR4 in breast cancer and adjacent non-cancerous tissue were statistically significant. We found a negative correlation between the expression of SATB1 and TLR4 (r=−0.624, P<0.05). The expression of SATB1 and TLR4 were not significantly correlated with age, menopause, and PR and HER-2 protein expression, but were significantly correlated with tumor size, local lymphatic metastasis, histopathological grade, tumor stage, and ER protein expression (P<0.05). Overall, SATB1 and TLR4 proteins are involved in the development of breast cancer, a finding of great significance to identify therapeutic targets and prognosis markers for breast cancer.
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Affiliation(s)
- Xuebo Wang
- Department of Clinical Laboratory, Yuhuangding Hospital of Yantai, Yantai, Shandong 264000, P.R. China
| | - Xiumei Yu
- Department of Clinical Laboratory, Yuhuangding Hospital of Yantai, Yantai, Shandong 264000, P.R. China
| | - Qingli Wang
- Department of Cardiology, The People's Hospital of Zhangqiu, Zhangqiu, Shandong 250200, P.R. China
| | - Yingying Lu
- Department of Clinical Laboratory, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China
| | - Haixia Chen
- Department of Clinical Laboratory, Yeda Hospital of Yantai, Yantai, Shandong 264000, P.R. China
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34
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Heilmann AM, Schrock AB, He J, Nahas M, Curran K, Shukla N, Cramer S, Draper L, Verma A, Erlich R, Ross J, Stephens P, Miller VA, Ali SM, Verglio JA, Tallman MS, Mughal TI. Novel PDGFRB fusions in childhood B- and T-acute lymphoblastic leukemia. Leukemia 2017; 31:1989-1992. [PMID: 28552906 DOI: 10.1038/leu.2017.161] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - A B Schrock
- Foundation Medicine Inc., Cambridge, MA, USA
| | - J He
- Foundation Medicine Inc., Cambridge, MA, USA
| | - M Nahas
- Foundation Medicine Inc., Cambridge, MA, USA
| | - K Curran
- Memorial Sloane Kettering Cancer Center, New York, NY, USA
| | - N Shukla
- Memorial Sloane Kettering Cancer Center, New York, NY, USA
| | - S Cramer
- University of Alabama, Birmingham, MS, USA
| | - L Draper
- University of Utah, Salt Lake City, UT, USA
| | - A Verma
- University of Utah, Salt Lake City, UT, USA
| | - R Erlich
- Foundation Medicine Inc., Cambridge, MA, USA
| | - J Ross
- Foundation Medicine Inc., Cambridge, MA, USA.,Albany College of Medicine, Albany, NY, USA
| | - P Stephens
- Foundation Medicine Inc., Cambridge, MA, USA
| | - V A Miller
- Foundation Medicine Inc., Cambridge, MA, USA
| | - S M Ali
- Foundation Medicine Inc., Cambridge, MA, USA
| | - J-A Verglio
- Foundation Medicine Inc., Cambridge, MA, USA
| | - M S Tallman
- Memorial Sloane Kettering Cancer Center, New York, NY, USA
| | - T I Mughal
- Foundation Medicine Inc., Cambridge, MA, USA.,Tufts University Medical Center, Boston, MA, USA
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