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Dawoud MM, Jones DT, Chelala C, Abdou AG, Dreger SA, Asaad N, Abd El-Wahed M, Jones L. Expression Profile of Myoepithelial Cells in DCIS: Do They Change From Protective Angels to Wicked Witches? Appl Immunohistochem Mol Morphol 2022; 30:397-409. [PMID: 35467556 DOI: 10.1097/pai.0000000000001028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/18/2022] [Indexed: 11/02/2022]
Abstract
The mechanism of transition of ductal carcinoma in situ (DCIS) to invasive cancer is elusive but recently changes in the myoepithelial cells (MECs) have been implicated. The aim of this study is to investigate the changes in gene profile of MECs in DCIS that could compromise their tumor suppressor function leading to promotion of tumor progression. Immuno-laser capture microdissection (LCM) was used to isolate MECs from normal and DCIS breast tissues followed by whole genome expression profiling using Affymetrix HGU-133 plus2.0 arrays. The data were analyzed using Bioconductor packages then validated by using real-time quantitative polymerase chain reaction and immunohistochemistry. Ingenuity Pathways software analysis showed clustering of most of the altered genes in cancer and cell death networks, with the Wnt/B-catenin pathway as the top canonical pathway. Validation revealed a 71.4% correlation rate with the array results. Most dramatic was upregulation of Fibronectin 1 ( FN1 ) in DCIS-associated MECs. Immunohistochemistry analysis for FN1 on normal and DCIS tissues confirmed a strong correlation between FN1 protein expression by MECs and DCIS ( P <0.0001) and between high expression level and presence of invasion ( P =0.006) in DCIS. Other validated alterations in MEC expression profile included upregulation of Nephronectin and downregulation of parathyroid hormone like hormone ( PTHLH ), fibroblast growth factor receptor 2 ( FGFR2 ), ADAMTS5 , TGFBR3 , and CAV1 . In vitro experiments revealed downregulation of PTHLH in DCIS-modified MECs versus normal lines when cultured on Fibronectin matrix. This is the first study to use this in vivo technique to investigate molecular changes in MECs in DCIS. This study adds more evidences to the molecular deviations in MECs toward tumor progression in DCIS through upregulation of the tumor-promoting molecules that may lead to novel predictive and therapeutic targets.
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Affiliation(s)
- Marwa M Dawoud
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Dylan T Jones
- Centre for Tumour Biology, Institute of Cancer & CR-UK Clinical Centre, Barts and The London School of Medicine & Dentistry, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ
| | - Claude Chelala
- Centre for Tumour Biology, Institute of Cancer & CR-UK Clinical Centre, Barts and The London School of Medicine & Dentistry, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ
| | - Asmaa G Abdou
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Sally A Dreger
- Centre for Tumour Biology, Institute of Cancer & CR-UK Clinical Centre, Barts and The London School of Medicine & Dentistry, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ
- Gut Microbes in Health, Quadram Institute Bioscience, Norwich, UK
| | - Nancy Asaad
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | | | - Louise Jones
- Centre for Tumour Biology, Institute of Cancer & CR-UK Clinical Centre, Barts and The London School of Medicine & Dentistry, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ
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2
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Li JX, Wang JJ, Deng ZF, Zheng H, Yang CM, Yuan Y, Yang C, Gu FF, Wu WQ, Qiao GL, Ma LJ. Circular RNA circ_0008934 promotes hepatocellular carcinoma growth and metastasis through modulating miR-1305/TMTC3 axis. Hum Cell 2022; 35:498-510. [PMID: 35015267 DOI: 10.1007/s13577-021-00657-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/30/2021] [Indexed: 11/29/2022]
Abstract
Circular RNAs (circRNAs) play important roles in the progression of hepatocellular carcinoma (HCC). However, the exact function of circ_0008934 in HCC is unknown. Our study aimed to investigate the expression characteristics of circ_0008934 in HCC and its effects on the proliferation and metastasis of HCC, and to explore the potential mechanism. In this study, circ_0008934 expression was found to be significantly upregulated in HCC tissues and cell lines by qRT-PCR. High level of circ_0008934 is closely associated with higher serum AFP (P < 0.001), larger tumor diameter (P = 0.012), microvascular invasion (P = 0.008) and poorer prognosis (P = 0.007) of HCC patients. Functionally, knockdown of circ_0008934 inhibited HCC cell proliferation, invasion and migration in vitro and vivo. Mechanically, circ_0008934 was a sponge of miR-1305 to facilitate the TMTC3 expression, and the TMTC3 expression in HCC tissues was negatively associated with the survival of HCC patients. Furthermore, rescued assays revealed that the circ_0008934 facilitated HCC proliferation, invasion and migration by regulating miR-1305/ TMTC3 signaling pathways. Overall, these results demonstrate that downregulation of circ_0008934 repress HCC growth and metastasis by upregulating miR-1305 to inhibit TMTC3, suggesting circ_0008934/ miR-1305/ TMTC3 regulatory axis may be a possible novel therapeutic target for HCC.
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Affiliation(s)
- Jia-Xi Li
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111, Xianxia Road, Shanghai, 200336, China
| | - Jin-Jiang Wang
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111, Xianxia Road, Shanghai, 200336, China
| | - Zhou-Feng Deng
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111, Xianxia Road, Shanghai, 200336, China
| | - Hao Zheng
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China.,The Department of Reproductive Genetic Center, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Chun-Mei Yang
- Department of Laboratory, Shunyi District Hospital, Beijing, 101300, China
| | - Ying Yuan
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111, Xianxia Road, Shanghai, 200336, China
| | - Cheng Yang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China
| | - Fang-Fang Gu
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111, Xianxia Road, Shanghai, 200336, China
| | - Wei-Qi Wu
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111, Xianxia Road, Shanghai, 200336, China.
| | - Guang-Lei Qiao
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111, Xianxia Road, Shanghai, 200336, China.
| | - Li-Jun Ma
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111, Xianxia Road, Shanghai, 200336, China.
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3
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Martinez-Morales P, Morán Cruz I, Roa-de la Cruz L, Maycotte P, Reyes Salinas JS, Vazquez Zamora VJ, Gutierrez Quiroz CT, Montiel-Jarquin AJ, Vallejo-Ruiz V. Hallmarks of glycogene expression and glycosylation pathways in squamous and adenocarcinoma cervical cancer. PeerJ 2021; 9:e12081. [PMID: 34540372 PMCID: PMC8415283 DOI: 10.7717/peerj.12081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
Background Dysregulation of glycogene expression in cancer can lead to aberrant glycan expression, which can promote tumorigenesis. Cervical cancer (CC) displays an increased expression of glycogenes involved in sialylation and sialylated glycans. Here, we show a comprehensive analysis of glycogene expression in CC to identify glycogene expression signatures and the possible glycosylation pathways altered. Methods First, we performed a microarray expression assay to compare glycogene expression changes between normal and cervical cancer tissues. Second, we used 401 glycogenes to analyze glycogene expression in adenocarcinoma and squamous carcinoma from RNA-seq data at the cBioPortal for Cancer Genomics. Results The analysis of the microarray expression assay indicated that CC displayed an increase in glycogenes related to GPI-anchored biosynthesis and a decrease in genes associated with chondroitin and dermatan sulfate with respect to normal tissue. Also, the glycogene analysis of CC samples by the RNA-seq showed that the glycogenes involved in the chondroitin and dermatan sulfate pathway were downregulated. Interestingly the adenocarcinoma tumors displayed a unique glycogene expression signature compared to squamous cancer that shows heterogeneous glycogene expression divided into six types. Squamous carcinoma type 5 (SCC-5) showed increased expression of genes implicated in keratan and heparan sulfate synthesis, glycosaminoglycan degradation, ganglio, and globo glycosphingolipid synthesis was related to poorly differentiated tumors and poor survival. Squamous carcinoma type 6 (SCC-6) displayed an increased expression of genes involved in chondroitin/dermatan sulfate synthesis and lacto and neolacto glycosphingolipid synthesis and was associated with nonkeratinizing squamous cancer and good survival. In summary, our study showed that CC tumors are not a uniform entity, and their glycome signatures could be related to different clinicopathological characteristics.
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Affiliation(s)
- Patricia Martinez-Morales
- CONACYT-Centro de Investigación Biomédica de Oriente, Mexican Institute of Social Security, Metepec, Puebla, México
| | - Irene Morán Cruz
- Centro de Investigación Biomédica de Oriente, Laboratory of Molecular Biology, Instituto Mexicano del Seguro Social, Metepec, Puebla, México
| | - Lorena Roa-de la Cruz
- Department of Biological Chemical Sciences, Universidad de las Américas-Puebla, San Andrés Cholula, Puebla, Mexico
| | - Paola Maycotte
- Centro de Investigación Biomédica de Oriente, Laboratory of Cell Biology, Instituto Mexicano del Seguro Social, Metepec, Puebla, México
| | - Juan Salvador Reyes Salinas
- Hospital de especialidades, General Manuel Ávila Camacho, Instituto Mexicano del Seguro Social, Puebla, Puebla, México
| | - Victor Javier Vazquez Zamora
- Hospital de especialidades, General Manuel Ávila Camacho, Instituto Mexicano del Seguro Social, Puebla, Puebla, México
| | | | - Alvaro Jose Montiel-Jarquin
- Hospital de especialidades, General Manuel Ávila Camacho, Instituto Mexicano del Seguro Social, Puebla, Puebla, México
| | - Verónica Vallejo-Ruiz
- Centro de Investigación Biomédica de Oriente, Laboratory of Molecular Biology, Instituto Mexicano del Seguro Social, Metepec, Puebla, México
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Savino A, De Marzo N, Provero P, Poli V. Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis. Cancers (Basel) 2021; 13:3371. [PMID: 34282769 PMCID: PMC8268805 DOI: 10.3390/cancers13133371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Transcriptome data provide a valuable resource for the study of cancer molecular mechanisms, but technical biases, sample heterogeneity, and small sample sizes result in poorly reproducible lists of regulated genes. Additionally, the presence of multiple cellular components contributing to cancer development complicates the interpretation of bulk transcriptomic profiles. To address these issues, we collected 48 microarray datasets derived from laser capture microdissected stroma or epithelium in breast tumors and performed a meta-analysis identifying robust lists of differentially expressed genes. This was used to create a database with carefully harmonized metadata that we make freely available to the research community. As predicted, combining the results of multiple datasets improved statistical power. Moreover, the separate analysis of stroma and epithelium allowed the identification of genes with different contributions in each compartment, which would not be detected by bulk analysis due to their distinct regulation in the two compartments. Our method can be profitably used to help in the discovery of biomarkers and the identification of functionally relevant genes in both the stroma and the epithelium. This database was made to be readily accessible through a user-friendly web interface.
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Affiliation(s)
- Aurora Savino
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy;
| | - Niccolò De Marzo
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy;
| | - Paolo Provero
- Department of Neurosciences “Rita Levi Montalcini”, University of Turin, Corso Massimo D’Azeglio 52, 10126 Turin, Italy;
- Center for Omics Sciences, Ospedale San Raffaele IRCCS, Via Olgettina 60, 20132 Milan, Italy
| | - Valeria Poli
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy;
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5
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El-Benhawy SA, Ebeid SA, Abd El Moneim NA, Arab ARR, Ramadan R. Repression of protocadherin 17 is correlated with elevated angiogenesis and hypoxia markers in female patients with breast cancer. Cancer Biomark 2021; 31:139-148. [PMID: 33896826 DOI: 10.3233/cbm-201593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Altered cadherin expression plays a vital role in tumorigenesis, angiogenesis and tumor progression. However, the function of protocadherin 17 (PCDH17) in breast cancer remains unclear. OBJECTIVE Our target is to explore PCDH17 gene expression in breast carcinoma tissues and its relation to serum angiopoietin-2 (Ang-2), carbonic anhydrase IX (CAIX) and % of circulating CD34+ cells in breast cancer patients (BCPs). METHODS This study included Fifty female BCPs and 50 healthy females as control group. Cancerous and neighboring normal breast tissues were collected from BCPs as well as blood samples at diagnosis. PCDH17 gene expression was evaluated by RT-PCR. Serum Ang-2, CAIX levels were measured by ELISA and % CD34+ cells were assessed by flow cytometry. RESULTS PCDH17 was downregulated in cancerous breast tissues and its repression was significantly correlated with advanced stage and larger tumor size. Low PCDH17 was significantly correlated with serum Ang-2, % CD34+ cells and serum CAIX levels. Serum CAIX, Ang-2 and % CD34+ cells levels were highly elevated in BCPs and significantly correlated with clinical stage. CONCLUSIONS PCDH17 downregulation correlated significantly with increased angiogenic and hypoxia biomarkers. These results explore the role of PCDH17 as a tumor suppressor gene inhibiting tumor growth and proliferation.
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Affiliation(s)
- Sanaa A El-Benhawy
- Radiation Sciences Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Samia A Ebeid
- Applied Medical Chemistry Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Nadia A Abd El Moneim
- Cancer Management and Research Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Amal R R Arab
- Applied Medical Chemistry Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Rabie Ramadan
- Experimental and Clinical Surgery Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
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6
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Xiao X, Zhang Z, Luo R, Peng R, Sun Y, Wang J, Chen X. Identification of potential oncogenes in triple-negative breast cancer based on bioinformatics analyses. Oncol Lett 2021; 21:363. [PMID: 33747220 PMCID: PMC7967975 DOI: 10.3892/ol.2021.12624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/02/2021] [Indexed: 12/28/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a subtype with high rates of metastasis, poor prognosis and limited therapeutic options. The present study aimed to identify the potential pivotal genes for prognosis and treatment in TNBC. A total of two microarray expression datasets, GSE38959 and GSE65212, were downloaded from the Gene Expression Omnibus database, and RNA-sequencing data of breast cancer from The Cancer Genome Atlas database were analyzed to screen out differentially expressed genes (DEGs) between TNBC tissues and normal tissues. The intersection of DEGs was submitted to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. A protein-protein interaction (PPI) network was constructed and visualized using Cytoscape software. Furthermore, module, centrality and survival analyses were performed to identify the potential hub genes. Reverse transcription-quantitative (RT-q)PCR analysis was performed to detect the expression levels of key genes in TNBC samples, and 377 DEGs were identified. Functional analysis revealed that the DEGs were significantly involved in cell cycle process, nuclear division and the p53 signaling pathway. A PPI network was constructed with these DEGs, and 66 core genes with high centrality features in module 1 were selected. Relapse-free survival analysis confirmed that high expression levels of five genes [cyclin B1 (CCNB1), GINS complex subunit 2, non-SMC condensin I complex subunit G (NCAPG), minichromosome maintenance 4 (MCM4) and ribonucleotide reductase regulatory subunit M2 (RRM2)] were significantly associated with poor prognosis in TNBC. RT-qPCR analysis demonstrated that CCNB1, NCAPG, MCM4 and RRM2 were significantly upregulated in 25 TNBC tissues compared with adjacent normal breast tissues. Furthermore, gene set enrichment analysis revealed that CCNB1, NCAPG, MCM4 and RRM2 were closely associated with tumor proliferation. Taken together, these results suggest that CCNB1, NCAPG, MCM4 and RRM2 are associated with tumorigenesis and TNBC progression, and thus may act as promising prognostic biomarkers and therapeutic targets for TNBC.
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Affiliation(s)
- Xiao Xiao
- Department of Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China
| | - Zheng Zhang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Ruihan Luo
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Rui Peng
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yan Sun
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Jia Wang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xin Chen
- Department of Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China
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7
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Yu M, Xu W, Jie Y, Pang J, Huang S, Cao J, Gong J, Li X, Chong Y. Identification and validation of three core genes in p53 signaling pathway in hepatitis B virus-related hepatocellular carcinoma. World J Surg Oncol 2021; 19:66. [PMID: 33685467 PMCID: PMC7938465 DOI: 10.1186/s12957-021-02174-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common cancer and the leading cause is persistent hepatitis B virus (HBV) infection. We aimed to identify some core genes and pathways for HBV-related HCC. METHODS Gene expression profiles of GSE62232, GSE121248, and GSE94660 were available from Gene Expression Omnibus (GEO). The GSE62232 and GSE121248 profiles were the analysis datasets and GSE94660 was the validation dataset. The GEO2R online tool and Venn diagram software were applied to analyze commonly differentially expressed genes between HBV-related HCC tissues and normal tissues. Then, functional enrichment analysis using Gene Ontology (GO) and the Kyoto Encyclopedia of Gene and Genome (KEGG) as well as the protein-protein interaction (PPI) network was conducted. The overall survival rates and the expression levels were detected by Kaplan-Meier plotter and Gene Expression Profiling Interactive Analysis (GEPIA). Next, gene set enrichment analysis (GSEA) was performed to verify the KEGG pathway analysis. Furthermore, quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) was performed to validate the levels of these three core genes in tumor tissues and adjacent non-tumor liver tissues from 12 HBV related HCC patients, HBV-associated liver cancer cell lines and normal liver cell lines, and HepG2 with p53 knockdown or deletion, respectively. RESULTS Fifteen highly expressed genes associated with significantly worse prognoses were selected and CCNB1, CDK1, and RRM2 in the p53 signaling pathway were identified as core genes. GSEA results showed that samples highly expressing three core genes were all enriched in the p53 signaling pathway in a validation dataset (P < 0.0001). The expression of these three core genes in tumor tissue samples was higher than that in relevant adjacent non-tumor liver tissues (P < 0.0001). Furthermore, we also found that the above genes were highly expressed in liver cancer cell lines compared with normal liver cells. In addition, we found that the expression of these three core genes in p53 knockdown or knockout HCC cell lines was lower than that in negative control HCC cell lines (P < 0.05). CONCLUSIONS CCNB1, CDK1, and RRM2 were enriched in the p53 signaling pathway and could be potential biomarkers and therapeutic targets for HBV-related HCC.
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Affiliation(s)
- Mingxue Yu
- Department of Infectious Diseases and Key Laboratory of Liver Disease of Guangdong Province, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, Guangdong Province, China
| | - Wenli Xu
- Department of Infectious Diseases and Key Laboratory of Liver Disease of Guangdong Province, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, Guangdong Province, China
| | - Yusheng Jie
- Department of Infectious Diseases and Key Laboratory of Liver Disease of Guangdong Province, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, Guangdong Province, China
| | - Jiahui Pang
- Department of Infectious Diseases and Key Laboratory of Liver Disease of Guangdong Province, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, Guangdong Province, China
| | - Siqi Huang
- Department of Infectious Diseases and Key Laboratory of Liver Disease of Guangdong Province, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, Guangdong Province, China
| | - Jing Cao
- Department of Infectious Diseases and Key Laboratory of Liver Disease of Guangdong Province, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, Guangdong Province, China
| | - Jiao Gong
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, Guangdong Province, China
| | - Xinhua Li
- Department of Infectious Diseases and Key Laboratory of Liver Disease of Guangdong Province, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, Guangdong Province, China.
| | - Yutian Chong
- Department of Infectious Diseases and Key Laboratory of Liver Disease of Guangdong Province, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, Guangdong Province, China.
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8
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Boujemaa M, Hamdi Y, Mejri N, Romdhane L, Ghedira K, Bouaziz H, El Benna H, Labidi S, Dallali H, Jaidane O, Ben Nasr S, Haddaoui A, Rahal K, Abdelhak S, Boussen H, Boubaker MS. Germline copy number variations in BRCA1/2 negative families: Role in the molecular etiology of hereditary breast cancer in Tunisia. PLoS One 2021; 16:e0245362. [PMID: 33503040 PMCID: PMC7840007 DOI: 10.1371/journal.pone.0245362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
Hereditary breast cancer accounts for 5-10% of all breast cancer cases. So far, known genetic risk factors account for only 50% of the breast cancer genetic component and almost a quarter of hereditary cases are carriers of pathogenic mutations in BRCA1/2 genes. Hence, the genetic basis for a significant fraction of familial cases remains unsolved. This missing heritability may be explained in part by Copy Number Variations (CNVs). We herein aimed to evaluate the contribution of CNVs to hereditary breast cancer in Tunisia. Whole exome sequencing was performed for 9 BRCA negative cases with a strong family history of breast cancer and 10 matched controls. CNVs were called using the ExomeDepth R-package and investigated by pathway analysis and web-based bioinformatic tools. Overall, 483 CNVs have been identified in breast cancer patients. Rare CNVs affecting cancer genes were detected, of special interest were those disrupting APC2, POU5F1, DOCK8, KANSL1, TMTC3 and the mismatch repair gene PMS2. In addition, common CNVs known to be associated with breast cancer risk have also been identified including CNVs on APOBECA/B, UGT2B17 and GSTT1 genes. Whereas those disrupting SULT1A1 and UGT2B15 seem to correlate with good clinical response to tamoxifen. Our study revealed new insights regarding CNVs and breast cancer risk in the Tunisian population. These findings suggest that rare and common CNVs may contribute to disease susceptibility. Those affecting mismatch repair genes are of interest and require additional attention since it may help to select candidates for immunotherapy leading to better outcomes.
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Affiliation(s)
- Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Biology, Faculty of Science of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Houda El Benna
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Olfa Jaidane
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Sonia Ben Nasr
- Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | | | - Khaled Rahal
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
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9
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Ciesielski O, Biesiekierska M, Panthu B, Vialichka V, Pirola L, Balcerczyk A. The Epigenetic Profile of Tumor Endothelial Cells. Effects of Combined Therapy with Antiangiogenic and Epigenetic Drugs on Cancer Progression. Int J Mol Sci 2020; 21:ijms21072606. [PMID: 32283668 PMCID: PMC7177242 DOI: 10.3390/ijms21072606] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023] Open
Abstract
Tumors require a constant supply of nutrients to grow which are provided through tumor blood vessels. To metastasize, tumors need a route to enter circulation, that route is also provided by tumor blood vessels. Thus, angiogenesis is necessary for both tumor progression and metastasis. Angiogenesis is tightly regulated by a balance of angiogenic and antiangiogenic factors. Angiogenic factors of the vascular endothelial growth factor (VEGF) family lead to the activation of endothelial cells, proliferation, and neovascularization. Significant VEGF-A upregulation is commonly observed in cancer cells, also due to hypoxic conditions, and activates endothelial cells (ECs) by paracrine signaling stimulating cell migration and proliferation, resulting in tumor-dependent angiogenesis. Conversely, antiangiogenic factors inhibit angiogenesis by suppressing ECs activation. One of the best-known anti-angiogenic factors is thrombospondin-1 (TSP-1). In pathological angiogenesis, the balance shifts towards the proangiogenic factors and an angiogenic switch that promotes tumor angiogenesis. Here, we review the current literature supporting the notion of the existence of two different endothelial lineages: normal endothelial cells (NECs), representing the physiological form of vascular endothelium, and tumor endothelial cells (TECs), which are strongly promoted by the tumor microenvironment and are biologically different from NECs. The angiogenic switch would be also important for the explanation of the differences between NECs and TECs, as angiogenic factors, cytokines and growth factors secreted into the tumor microenvironment may cause genetic instability. In this review, we focus on the epigenetic differences between the two endothelial lineages, which provide a possible window for pharmacological targeting of TECs.
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Affiliation(s)
- Oskar Ciesielski
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (O.C.); (M.B.); (V.V.)
- The Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Marta Biesiekierska
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (O.C.); (M.B.); (V.V.)
| | - Baptiste Panthu
- INSERM Unit 1060, CarMeN Laboratory, Lyon 1 University, 165 Chemin du Grand Revoyet—BP12, F-69495 Pierre Bénite CEDEX, France; (B.P.); (L.P.)
| | - Varvara Vialichka
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (O.C.); (M.B.); (V.V.)
| | - Luciano Pirola
- INSERM Unit 1060, CarMeN Laboratory, Lyon 1 University, 165 Chemin du Grand Revoyet—BP12, F-69495 Pierre Bénite CEDEX, France; (B.P.); (L.P.)
| | - Aneta Balcerczyk
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (O.C.); (M.B.); (V.V.)
- Correspondence: ; Tel.: +48-42-635-45-10
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Yang D, He Y, Wu B, Deng Y, Wang N, Li M, Liu Y. Integrated bioinformatics analysis for the screening of hub genes and therapeutic drugs in ovarian cancer. J Ovarian Res 2020; 13:10. [PMID: 31987036 PMCID: PMC6986075 DOI: 10.1186/s13048-020-0613-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/20/2020] [Indexed: 02/06/2023] Open
Abstract
Background Ovarian cancer (OC) ranks fifth as a cause of gynecological cancer-associated death globally. Until now, the molecular mechanisms underlying the tumorigenesis and prognosis of OC have not been fully understood. This study aims to identify hub genes and therapeutic drugs involved in OC. Methods Four gene expression profiles (GSE54388, GSE69428, GSE36668, and GSE40595) were downloaded from the Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) in OC tissues and normal tissues with an adjusted P-value < 0.05 and a |log fold change (FC)| > 1.0 were first identified by GEO2R and FunRich software. Next, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses were performed for functional enrichment analysis of these DEGs. Then, the hub genes were identified by the cytoHubba plugin and the other bioinformatics approaches including protein-protein interaction (PPI) network analysis, module analysis, survival analysis, and miRNA-hub gene network construction was also performed. Finally, the GEPIA2 and DGIdb databases were utilized to verify the expression levels of hub genes and to select the candidate drugs for OC, respectively. Results A total of 171 DEGs were identified, including 114 upregulated and 57 downregulated DEGs. The results of the GO analysis indicated that the upregulated DEGs were mainly involved in cell division, nucleus, and protein binding, whereas the biological functions showing enrichment in the downregulated DEGs were mainly negative regulation of transcription from RNA polymerase II promoter, protein complex and apicolateral plasma membrane, and glycosaminoglycan binding. As for the KEGG-pathway, the upregulated DEGs were mainly associated with metabolic pathways, biosynthesis of antibiotics, biosynthesis of amino acids, cell cycle, and HTLV-I infection. Additionally, 10 hub genes (KIF4A, CDC20, CCNB2, TOP2A, RRM2, TYMS, KIF11, BIRC5, BUB1B, and FOXM1) were identified and survival analysis of these hub genes showed that OC patients with the high-expression of CCNB2, TYMS, KIF11, KIF4A, BIRC5, BUB1B, FOXM1, and CDC20 were statistically more likely to have poorer progression free survival. Meanwhile, the expression levels of the hub genes based on GEPIA2 were in accordance with those based on GEO. Finally, DGIdb database was used to identify 62 small molecules as the potentially targeted drugs for OC treatment. Conclusions In summary, the data may produce new insights regarding OC pathogenesis and treatment. Hub genes and candidate drugs may improve individualized diagnosis and therapy for OC in future.
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Affiliation(s)
- Dan Yang
- Department of Environmental Health, School of Public Health, China Medical University, 77th Puhe Road, Shenyang, 110122, Liaoning, China
| | - Yang He
- Department of Central Laboratory, The First Affiliated Hospital, China Medical University, 155th Nanjing North Street, Shenyang, 110001, Liaoning, China
| | - Bo Wu
- Department of Anus and Intestine Surgery, The First Affiliated Hospital, China Medical University, 155th Nanjing North Street, Shenyang, 110001, Liaoning, China
| | - Yan Deng
- Department of Environmental Health, School of Public Health, China Medical University, 77th Puhe Road, Shenyang, 110122, Liaoning, China
| | - Nan Wang
- Department of Environmental Health, School of Public Health, China Medical University, 77th Puhe Road, Shenyang, 110122, Liaoning, China
| | - Menglin Li
- Department of Environmental Health, School of Public Health, China Medical University, 77th Puhe Road, Shenyang, 110122, Liaoning, China
| | - Yang Liu
- Department of Environmental Health, School of Public Health, China Medical University, 77th Puhe Road, Shenyang, 110122, Liaoning, China.
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Kovacheva M, Zepp M, Schraad M, Berger S, Berger MR. Conditional Knockdown of Osteopontin Inhibits Breast Cancer Skeletal Metastasis. Int J Mol Sci 2019; 20:E4918. [PMID: 31590218 PMCID: PMC6801824 DOI: 10.3390/ijms20194918] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/28/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023] Open
Abstract
High osteopontin (OPN) expression is linked to breast cancer bone metastasis. In this study we modulated osteopontin levels conditionally and investigated any related antineoplastic effects. Therefore, we established cell clones from human breast cancer MDA-MB-231 cells, in which the expression of OPN is regulated by the Tet-Off tet-off system. These cells, which conditionally express a specific miRNA targeting OPN, were used for in vitro studies as well as for a bone metastasis model in nude rats. Changes in whole-genome expression elicited by conditional OPN knockdown and vesicle formation were also analyzed. The alkylphosphocholine erufosine was used for combination therapy. Conditional OPN knockdown caused mild anti-proliferative, but more intensive anti-migratory and anti clonogenic effects, as well as partial and complete remissions of soft tissue and osteolytic lesions. These effects were associated with specific gene and protein expression modulations following miRNA-mediated OPN knockdown. Furthermore, high levels of OPN were detected in vesicles derived from rats harboring breast cancer skeletal metastases. Finally, the combination of OPN inhibition and erufosine treatment caused an additive reduction of OPN levels in the investigated breast cancer cells. Thus, knockdown of OPN alone or in combination with erufosine is a promising strategy in breast cancer skeletal metastasis treatment.
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Affiliation(s)
- Marineta Kovacheva
- German Cancer Research Center (DKFZ), Toxicology and Chemotherapy Unit, 69120 Heidelberg, Germany.
| | - Michael Zepp
- German Cancer Research Center (DKFZ), Toxicology and Chemotherapy Unit, 69120 Heidelberg, Germany.
| | - Muriel Schraad
- German Cancer Research Center (DKFZ), Toxicology and Chemotherapy Unit, 69120 Heidelberg, Germany.
| | - Stefan Berger
- Central Institute of Mental Health, Department of Molecular Biology, 68159 Mannheim, Germany.
| | - Martin R Berger
- German Cancer Research Center (DKFZ), Toxicology and Chemotherapy Unit, 69120 Heidelberg, Germany.
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EZH2 cooperates with E2F1 to stimulate expression of genes involved in adrenocortical carcinoma aggressiveness. Br J Cancer 2019; 121:384-394. [PMID: 31363169 PMCID: PMC6738105 DOI: 10.1038/s41416-019-0538-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/03/2019] [Accepted: 07/11/2019] [Indexed: 11/08/2022] Open
Abstract
Background EZH2 is overexpressed and associated with poor prognosis in adrenocortical carcinoma (ACC) and its inhibition reduces growth and aggressiveness of ACC cells in culture. Although EZH2 was identified as the methyltransferase that deposits the repressive H3K27me3 histone mark, it can cooperate with transcription factors to stimulate gene transcription. Methods We used bioinformatics approaches on gene expression data from three cohorts of patients and a mouse model of EZH2 ablation, to identify targets and mode of action of EZH2 in ACC. This was followed by ChIP and functional assays to evaluate contribution of identified targets to ACC pathogenesis. Results We show that EZH2 mostly works as a transcriptional inducer in ACC, through cooperation with the transcription factor E2F1 and identify three positive targets involved in cell cycle regulation and mitosis i.e., RRM2, PTTG1 and ASE1/PRC1. Overexpression of these genes is associated with poor prognosis, suggesting a potential role in acquisition of aggressive ACC features. Pharmacological and siRNA-mediated inhibition of RRM2 blocks cell proliferation, induces apoptosis and inhibits cell migration, suggesting that it may be an interesting target in ACC. Conclusions Altogether, these data show an unexpected role of EZH2 and E2F1 in stimulating expression of genes associated with ACC aggressiveness.
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Yang B, Pan CS, Li Q, Yang Z, Long FX, Fan JY, Wang CS, Han JY, Tang DX. Inhibitory effects of Chanling Gao on the proliferation and liver metastasis of transplanted colorectal cancer in nude mice. PLoS One 2019; 14:e0201504. [PMID: 30789971 PMCID: PMC6383928 DOI: 10.1371/journal.pone.0201504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/31/2019] [Indexed: 12/20/2022] Open
Abstract
This study aimed to explore the efficacy and mechanism of Chanling Gao (CLG), a compound Chinese medicine, on colorectal cancer (CRC). A model of transplanted CRC was established in nude mice. The mice were treated 7 days after CRC transplantation with either Capecitabine or CLG for 3 weeks. On the 28th day after the operation, CRC growth and liver metastasis were assessed by morphology, the changes in the expression of HIF-1α (hypoxia inducible factor-1α), stromal cell-derived factor-1 alpha (SDF-1α), CXCR4 (C-X-C chemokine receptor type 4), PI3K, and Akt in the transplanted tumor and SDF-1α and CXCR4 in the liver were detected by Western blot and immunohistochemistry. The protein contents of vascular endothelial growth factor (VEGF), matrix metalloproteinase (MMP)-2, and collagen IV in the serum and transplanted tumor and SDF-1α and CXCR4 in liver tissues were detected by enzyme-linked immunosorbent assay. In the Capecitabine and high dose CLG groups, the growth and liver metastasis of CRC were significantly inhibited, the protein levels of HIF-1α, SDF-1α, CXCR4, MMP-2, VEGF, PI3K, Akt, P-PI3K and P-Akt in the transplanted tumor were lower, while the content of collagen IV in the transplanted tumor was higher, than in Model group. A high dose of CLG inhibited the growth of transplanted tumor and liver metastasis of CRC in nude mice, probably by inhibiting the HIF-1α/SDF-1α-CXCR4/PI3K-Akt signaling pathway reducing the synthesis and release of VEGF and degradation of collagen IV.
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Affiliation(s)
- Bing Yang
- Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Chun-Shui Pan
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China
| | - Quan Li
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China
| | - Zhu Yang
- Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Feng-Xi Long
- Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Jing-Yu Fan
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China
| | - Chuan-She Wang
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Jing-Yan Han
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Dong-Xin Tang
- Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- Department of Oncology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
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Patra P, Izawa T, Pena-Castillo L. REPA: Applying Pathway Analysis to Genome-Wide Transcription Factor Binding Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1270-1283. [PMID: 27019499 DOI: 10.1109/tcbb.2015.2453948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Pathway analysis has been extensively applied to aid in the interpretation of the results of genome-wide transcription profiling studies, and has been shown to successfully find associations between the biological phenomena under study and biological pathways. There are two widely used approaches of pathway analysis: over-representation analysis, and gene set analysis. Recently genome-wide transcription factor binding data has become widely available allowing for the application of pathway analysis to this type of data. In this work, we developed regulatory enrichment pathway analysis (REPA) to apply gene set analysis to genome-wide transcription factor binding data to infer associations between transcription factors and biological pathways. We used the transcription factor binding data generated by the ENCODE project, and gene sets from the Molecular Signatures and KEGG databases. Our results showed that 54 percent of the predictions examined have literature support and that REPA's recall is roughly 54 percent. This level of precision is promising as several of REPA's predictions are expected to be novel and can be used to guide new research avenues. In addition, the results of our case studies showed that REPA enhances the interpretation of genome-wide transcription profiling studies by suggesting putative regulators behind the observed transcriptional responses.
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Apelin: A putative novel predictive biomarker for bevacizumab response in colorectal cancer. Oncotarget 2018; 8:42949-42961. [PMID: 28487489 PMCID: PMC5522118 DOI: 10.18632/oncotarget.17306] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/04/2017] [Indexed: 12/17/2022] Open
Abstract
Bevacizumab (bvz) is currently employed as an anti-angiogenic therapy across several cancer indications. Bvz response heterogeneity has been well documented, with only 10-15% of colorectal cancer (CRC) patients benefitting in general. For other patients, clinical efficacy is limited and side effects are significant. This reinforces the need for a robust predictive biomarker of response. To identify such a biomarker, we performed a DNA microarray-based transcriptional profiling screen with primary endothelial cells (ECs) isolated from normal and tumour colon tissues. Thirteen separate populations of tumour-associated ECs and 10 of normal ECs were isolated using fluorescence-activated cell sorting. We hypothesised that VEGF-induced genes were overexpressed in tumour ECs; these genes could relate to bvz response and serve as potential predictive biomarkers. Transcriptional profiling revealed a total of 2,610 differentially expressed genes when tumour and normal ECs were compared. To explore their relation to bvz response, the mRNA expression levels of top-ranked genes were examined using quantitative PCR in 30 independent tumour tissues from CRC patients that received bvz in the adjuvant setting. These analyses revealed that the expression of MMP12 and APLN mRNA was significantly higher in bvz non-responders compared to responders. At the protein level, high APLN expression was correlated with poor progression-free survival in bvz-treated patients. Thus, high APLN expression may represent a novel predictive biomarker for bvz unresponsiveness.
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Hao Q, Zhao X, Zhang Y, Dong Z, Hu T, Chen P. Targeting Overexpressed Activating Transcription Factor 1 (ATF1) Inhibits Proliferation and Migration and Enhances Sensitivity to Paclitaxel In Esophageal Cancer Cells. Med Sci Monit Basic Res 2017; 23:304-312. [PMID: 28912415 PMCID: PMC5612263 DOI: 10.12659/msmbr.906289] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Previous reports showed that Activating Transcription Factor 1 (ATF1) plays an important role in tumor progression in a tumor-specific manner. However, little is known about the expression and role of ATF1 in esophageal cancer. Material/Methods The expression of ATF1 was examined by immunohistochemistry and Western blotting. The correlation between the expression of ATF1 and clinical characteristics of esophageal squamous cell carcinomas (ESCC) patients was analyzed by Fisher’s exact test. The role of cell proliferation, clonogenic survival, migration, and invasion in vitro, as well as the sensitization to paclitaxel, were determined after knockdown of ATF1 by siRNA. Results ATF1 was overexpressed in ESCC tissues, which was positively correlated with lymph node metastasis, poor differentiation, and early tumor invasion of esophageal cancer patients. Knockdown of ATF1 effectively reduced cell proliferation, induced S phase cell cycle arrest, and inhibited cell migration and invasion. Moreover, silencing of ATF1 significantly enhanced the sensitivity of esophageal cancer cells to paclitaxel. Conclusions These findings suggest that ATF1 is a promising drug target for esophageal cancer.
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Affiliation(s)
- Qianyun Hao
- College of Basic Medical Sciences, Zhengzhou University; Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China (mainland)
| | - Xuesong Zhao
- College of Basic Medical Sciences, Zhengzhou University; Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China (mainland)
| | - Yi Zhang
- College of Basic Medical Sciences, Zhengzhou University; Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China (mainland)
| | - Ziming Dong
- College of Basic Medical Sciences, Zhengzhou University; Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China (mainland)
| | - Tao Hu
- College of Basic Medical Sciences, Zhengzhou University; Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China (mainland)
| | - Ping Chen
- College of Basic Medical Sciences, Zhengzhou University; Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China (mainland)
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Modulated cellular delivery of anti-VEGF siRNA (bevasiranib) by incorporating supramolecular assemblies of hydrophobically modified polyamidoamine dendrimer in stealth liposomes. Int J Pharm 2016; 510:30-41. [PMID: 27291973 DOI: 10.1016/j.ijpharm.2016.06.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 12/16/2022]
Abstract
A novel lipopolymer based system was designed and characterized for cellular delivery of anti-VEGF siRNA in SKBR-3 breast tumor cell line. Polyamidoamine (PAMAM) dendrimers of low generations (G1, G2 and G3) were incorporated into polyethylene glycol (PEG)-stabilized liposomes by following the consecutive steps: (a) synthesis of the cholesterol conjugates (40% molar ratio of cholesterol to primary amines of PAMAM), (b) incorporation of the conjugates in liposome by lipid mixing and (c) microencapsulation of the siRNA using the ethanol drop method. The cholesterol conjugates of PAMAM dendrimers (G1-Chol40%, G2-Chol40% and G3-Chol40%) formed self assembly with low CMC values (<11μg/ml). Not only did G2-Chol40% show the highest lipid mixing among the cholesterol conjugates, but also, had the lowest leakage of encapsulated carboxyfluorescein tracer. Various N(amine))/L(lipid)/P(phosphate) mole ratios were investigated for siRNA condensation by ethidium bromide dye exclusion assay. The optimum N/L/P ratio of 20:33:10 was chosen for microencapsulation of anti-VEGF siRNA by ethanol drop method, showing particle size of 130nm, zeta-potential of +4mV, siRNA loading efficiency and capacity of 96% and 13wt%, and high stability against heparin sulfate (extracellular matrix). TEM shows uniform and discrete oligo- or multi-lamellar vesicular structures. The liposome incorporating G2-Chol40% was successfully internalized into SKBR-3 cells mainly through clathrin-mediated endocytosis, which was able to escape from endosomes and showed a significantly higher sequence-specific inhibition of VEGF expression and cell growth than the respective G2-Chol40%/siRNA dendriplexes. Importantly, the cytotoxicity decreased with incorporation of G2-Chol40% in the liposomes.
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de Camargo GMF, Aspilcueta-Borquis RR, Fortes MRS, Porto-Neto R, Cardoso DF, Santos DJA, Lehnert SA, Reverter A, Moore SS, Tonhati H. Prospecting major genes in dairy buffaloes. BMC Genomics 2015; 16:872. [PMID: 26510479 PMCID: PMC4625573 DOI: 10.1186/s12864-015-1986-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 10/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Asian buffaloes (Bubalus bubalis) have an important socio-economic role. The majority of the population is situated in developing countries. Due to the scarce resources in these countries, very few species-specific biotechnology tools exist and a lot of cattle-derived technologies are applied to buffaloes. However, the application of cattle genomic tools to buffaloes is not straightforward and, as results suggested, despite genome sequences similarity the genetic polymorphisms are different. RESULTS The first SNP chip genotyping platform designed specifically for buffaloes has recently become available. Herein, a genome-wide association study (GWAS) and gene network analysis carried out in buffaloes is presented. Target phenotypes were six milk production and four reproductive traits. GWAS identified SNP with significant associations and suggested candidate genes that were specific to each trait and also genes with pleiotropic effect, associated to multiple traits. CONCLUSIONS Network predictions of interactions between these candidate genes may guide further molecular analyses in search of disruptive mutations, help select genes for functional experiments and evidence metabolism differences in comparison to cattle. The cattle SNP chip does not offer an optimal coverage of buffalo genome, thereafter the development of new buffalo-specific genetic technologies is warranted. An annotated reference genome would greatly facilitate genetic research, with potential impact to buffalo-based dairy production.
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Affiliation(s)
- G M F de Camargo
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
| | - R R Aspilcueta-Borquis
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
| | - M R S Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - R Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, Brisbane, QLD, 4072, Australia.
| | - D F Cardoso
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
| | - D J A Santos
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
| | - S A Lehnert
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, Brisbane, QLD, 4072, Australia.
| | - A Reverter
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, Brisbane, QLD, 4072, Australia.
| | - S S Moore
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4067, Australia.
| | - H Tonhati
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
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Smith L, Baxter EW, Chambers PA, Green CA, Hanby AM, Hughes TA, Nash CE, Millican-Slater RA, Stead LF, Verghese ET, Speirs V. Down-Regulation of miR-92 in Breast Epithelial Cells and in Normal but Not Tumour Fibroblasts Contributes to Breast Carcinogenesis. PLoS One 2015; 10:e0139698. [PMID: 26437339 PMCID: PMC4593575 DOI: 10.1371/journal.pone.0139698] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/16/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND MicroRNA (miR) expression is commonly dysregulated in many cancers, including breast. MiR-92 is one of six miRs encoded by the miR-17-92 cluster, one of the best-characterised oncogenic miR clusters. We examined expression of miR-92 in the breast epithelium and stroma during breast cancer progression. We also investigated the role of miR-92 in fibroblasts in vitro and showed that down-regulation in normal fibroblasts enhances the invasion of breast cancer epithelial cells. METHODOLOGY/PRINCIPAL FINDINGS We used laser microdissection (LMD) to isolate epithelial cells from matched normal, DCIS and invasive tissue from 9 breast cancer patients and analysed miR-92 expression by qRT-PCR. Expression of ERβ1, a direct miR-92 target, was concurrently analysed for each case by immunohistochemistry. LMD was also used to isolate matched normal (NFs) and cancer-associated fibroblasts (CAFs) from 14 further cases. Effects of miR-92 inhibition in fibroblasts on epithelial cell invasion in vitro was examined using a Matrigel™ assay. miR-92 levels decreased in microdissected epithelial cells during breast cancer progression with highest levels in normal breast epithelium, decreasing in DCIS (p<0.01) and being lowest in invasive breast tissue (p<0.01). This was accompanied by a shift in cell localisation of ERβ1 from nuclear expression in normal breast epithelium to increased cytoplasmic expression during progression to DCIS (p = 0.0078) and invasive breast cancer (p = 0.031). ERβ1 immunoreactivity was also seen in stromal fibroblasts in tissues. Where miR-92 expression was low in microdissected NFs this increased in matched CAFs; a trend also seen in cultured primary fibroblasts. Down-regulation of miR-92 levels in NFs but not CAFs enhanced invasion of both MCF-7 and MDA-MB-231 breast cancer epithelial cells. CONCLUSIONS miR-92 is gradually lost in breast epithelial cells during cancer progression correlating with a shift in ERβ1 immunoreactivity from nuclei to the cytoplasm. Our data support a functional role in fibroblasts where modification of miR-92 expression can influence the invasive capacity of breast cancer epithelial cells. However in silico analysis suggests that ERβ1 may not be the most important miR-92 target in breast cancer.
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Affiliation(s)
- Laura Smith
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Euan W. Baxter
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Philip A. Chambers
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Caroline A. Green
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Andrew M. Hanby
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Thomas A. Hughes
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Claire E. Nash
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | | | - Lucy F. Stead
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Eldo T. Verghese
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Valerie Speirs
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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20
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Calderón-González KG, Valero Rustarazo ML, Labra-Barrios ML, Bazán-Méndez CI, Tavera-Tapia A, Herrera-Aguirre ME, Sánchez del Pino MM, Gallegos-Pérez JL, González-Márquez H, Hernández-Hernández JM, León-Ávila G, Rodríguez-Cuevas S, Guisa-Hohenstein F, Luna-Arias JP. Determination of the protein expression profiles of breast cancer cell lines by quantitative proteomics using iTRAQ labelling and tandem mass spectrometry. J Proteomics 2015; 124:50-78. [PMID: 25918110 DOI: 10.1016/j.jprot.2015.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED Breast cancer is the principal cancer in women worldwide. Although there are serum tumor markers such as CEA and HER2, they are detected in advanced stages of the disease and used as progression and recurrence markers. Therefore, there is a necessity for the identification of new markers that might lead to an early detection and also provide evidence of an effective treatment. The aim of this work was to determine the differential protein expression profiles of four breast cancer cell lines in comparison to a normal control cell line by iTRAQ labelling and tandem mass spectrometry, in order to identify putative biomarkers of the disease. We identified 1,020 iTRAQ-labelled polypeptides with at least one peptide identified with more than 95% in confidence. Overexpressed polypeptides in all cancer cell lines were 78, whilst the subexpressed were 128. We categorised them with PANTHER program into biological processes, being the metabolic pathways the most affected. We detected six groups of proteins with the STRING program involved in DNA topology, glycolysis, translation initiation, splicing, pentose pathway, and proteasome degradation. The main subexpressed protein network included mitochondrial proteins involved in oxidative phosphorylation. We propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer. BIOLOGICAL SIGNIFICANCE We report a set of differentially expressed proteins in the MCF7 and T47D (Luminal A), MDA-MB-231 (Claudin low) and SK-BR-3 (HER2(+)) breast cancer cell lines that have not been previously reported in breast cancer disease. From these proteins, we propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer. On the other hand, we propose sets of unique polypeptides in each breast cancer cell line that can be useful in the classification of different subtypes of breast cancer.
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Affiliation(s)
- Karla Grisel Calderón-González
- Doctorado en Ciencias Biológicas, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, C.P. 09340, México, D. F., México.
| | - Ma Luz Valero Rustarazo
- Unidad de Proteómica, Centro de Investigación Príncipe Felipe, C/Rambla del Saler 16, 46012 Valencia, España.
| | - Maria Luisa Labra-Barrios
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - César Isaac Bazán-Méndez
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Alejandra Tavera-Tapia
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Maria Esther Herrera-Aguirre
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Manuel M Sánchez del Pino
- Unidad de Proteómica, Centro de Investigación Príncipe Felipe, C/Rambla del Saler 16, 46012 Valencia, España.
| | | | - Humberto González-Márquez
- Doctorado en Ciencias Biológicas, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, C.P. 09340, México, D. F., México.
| | - Jose Manuel Hernández-Hernández
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Gloria León-Ávila
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Miguel Hidalgo, C.P. 11340, México, D. F., México.
| | - Sergio Rodríguez-Cuevas
- Instituto de Enfermedades de la Mama, Fundación del Cáncer de Mama (FUCAM A.C.), Av. Bordo No. 100, Col. Viejo Ejido de Santa Ursula Coapa, Coyoacán, C.P. 04980, México, D. F., México.
| | - Fernando Guisa-Hohenstein
- Instituto de Enfermedades de la Mama, Fundación del Cáncer de Mama (FUCAM A.C.), Av. Bordo No. 100, Col. Viejo Ejido de Santa Ursula Coapa, Coyoacán, C.P. 04980, México, D. F., México.
| | - Juan Pedro Luna-Arias
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
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21
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Zhuang X, Herbert JMJ, Lodhia P, Bradford J, Turner AM, Newby PM, Thickett D, Naidu U, Blakey D, Barry S, Cross DAE, Bicknell R. Identification of novel vascular targets in lung cancer. Br J Cancer 2015; 112:485-94. [PMID: 25535734 PMCID: PMC4453649 DOI: 10.1038/bjc.2014.626] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/13/2014] [Accepted: 11/26/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Lung cancer remains the leading cause of cancer-related death, largely owing to the lack of effective treatments. A tumour vascular targeting strategy presents an attractive alternative; however, the molecular signature of the vasculature in lung cancer is poorly explored. This work aimed to identify novel tumour vascular targets in lung cancer. METHODS Enzymatic digestion of fresh tissue followed by endothelial capture with Ulex lectin-coated magnetic beads was used to isolate the endothelium from fresh tumour specimens of lung cancer patients. Endothelial isolates from the healthy and tumour lung tissue were subjected to whole human genome expression profiling using microarray technology. RESULTS Bioinformatics analysis identified tumour endothelial expression of angiogenic factors, matrix metalloproteases and cell-surface transmembrane proteins. Predicted novel tumour vascular targets were verified by RNA-seq, quantitative real-time PCR analysis and immunohistochemistry. Further detailed expression profiling of STEAP1 on 82 lung cancer patients confirmed STEAP1 as a novel target in the tumour vasculature. Functional analysis of STEAP1 using siRNA silencing implicates a role in endothelial cell migration and tube formation. CONCLUSIONS The identification of cell-surface tumour endothelial markers in lung is of interest in therapeutic antibody and vaccine development.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Non-Small-Cell Lung/blood supply
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Endothelium, Vascular/metabolism
- Endothelium, Vascular/pathology
- Female
- Gene Expression Profiling
- Genetic Association Studies/methods
- Humans
- Lung/blood supply
- Lung/metabolism
- Lung/pathology
- Lung Neoplasms/blood supply
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Male
- Microarray Analysis
- Middle Aged
- Molecular Targeted Therapy
- Neovascularization, Pathologic/drug therapy
- Neovascularization, Pathologic/genetics
- Real-Time Polymerase Chain Reaction
- Sequence Analysis, RNA
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Affiliation(s)
- X Zhuang
- School of Immunity and Infection,
Institute for Biomedical Research, College of Medical and Dental Sciences,
University of Birmingham, Edgbaston, Birmingham
B15 2TT, UK
- School of Cancer Sciences, College of
Medical and Dental Sciences, University of Birmingham,
Edgbaston, Birmingham
B15 2TT, UK
| | - J M J Herbert
- School of Immunity and Infection,
Institute for Biomedical Research, College of Medical and Dental Sciences,
University of Birmingham, Edgbaston, Birmingham
B15 2TT, UK
- Technology Hub Sequencing and
Bioinformatics, College of Medical and Dental Sciences,
Birmingham
B15, UK
| | - P Lodhia
- School of Immunity and Infection,
Institute for Biomedical Research, College of Medical and Dental Sciences,
University of Birmingham, Edgbaston, Birmingham
B15 2TT, UK
| | - J Bradford
- AstraZeneca, Mereside,
Alderley Park, Macclesfield, Cheshire
SK10 4TG, UK
| | - A M Turner
- School of Clinical and Experimental
Medicine, University of Birmingham, QEHB Research Laboratories,
Mindelsohn Way, Birmingham
B15 2WB, UK
- Birmingham Heartlands Hospital,
Bordesley Green, Birmingham
B9 5SS, UK
| | - P M Newby
- School of Immunity and Infection,
Institute for Biomedical Research, College of Medical and Dental Sciences,
University of Birmingham, Edgbaston, Birmingham
B15 2TT, UK
| | - D Thickett
- School of Clinical and Experimental
Medicine, University of Birmingham, QEHB Research Laboratories,
Mindelsohn Way, Birmingham
B15 2WB, UK
| | - U Naidu
- School of Clinical and Experimental
Medicine, University of Birmingham, QEHB Research Laboratories,
Mindelsohn Way, Birmingham
B15 2WB, UK
- Birmingham Heartlands Hospital,
Bordesley Green, Birmingham
B9 5SS, UK
| | - D Blakey
- AstraZeneca, Mereside,
Alderley Park, Macclesfield, Cheshire
SK10 4TG, UK
| | - S Barry
- AstraZeneca, Mereside,
Alderley Park, Macclesfield, Cheshire
SK10 4TG, UK
| | - D A E Cross
- AstraZeneca, Mereside,
Alderley Park, Macclesfield, Cheshire
SK10 4TG, UK
| | - R Bicknell
- School of Immunity and Infection,
Institute for Biomedical Research, College of Medical and Dental Sciences,
University of Birmingham, Edgbaston, Birmingham
B15 2TT, UK
- School of Cancer Sciences, College of
Medical and Dental Sciences, University of Birmingham,
Edgbaston, Birmingham
B15 2TT, UK
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22
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Luo W, Hu Q, Wang D, Deeb KK, Ma Y, Morrison CD, Liu S, Johnson CS, Trump DL. Isolation and genome-wide expression and methylation characterization of CD31+ cells from normal and malignant human prostate tissue. Oncotarget 2014; 4:1472-83. [PMID: 23978847 PMCID: PMC3824530 DOI: 10.18632/oncotarget.1269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Endothelial cells (ECs) are an important component involved in the angiogenesis. Little is known about the global gene expression and epigenetic regulation in tumor endothelial cells. The identification of gene expression and epigenetic difference between human prostate tumor-derived endothelial cells (TdECs) and those in normal tissues may uncover unique biological features of TdEC and facilitate the discovery of new anti-angiogenic targets. We established a method for isolation of CD31+ endothelial cells from malignant and normal prostate tissues obtained at prostatectomy. TdECs and normal-derived ECs (NdECs) showed >90% enrichment in primary culture and demonstrated microvascular endothelial cell characteristics such as cobblestone morphology in monolayer culture, diI-acetyl-LDL uptake and capillary-tube like formation in Matrigel®. In vitro primary cultures of ECs maintained expression of endothelial markers such as CD31, von Willebrand factor, intercellular adhesion molecule, vascular endothelial growth factor receptor 1, and vascular endothelial growth factor receptor 2. We then conducted a pilot study of transcriptome and methylome analysis of TdECs and matched NdECs from patients with prostate cancer. We observed a wide spectrum of differences in gene expression and methylation patterns in endothelial cells, between malignant and normal prostate tissues. Array-based expression and methylation data were validated by qRT-PCR and bisulfite DNA pyrosequencing. Further analysis of transcriptome and methylome data revealed a number of differentially expressed genes with loci whose methylation change is accompanied by an inverse change in gene expression. Our study demonstrates the feasibility of isolation of ECs from histologically normal prostate and prostate cancer via CD31+ selection. The data, although preliminary, indicates that there exist widespread differences in methylation and transcription between TdECs and NdECs. Interestingly, only a small proportion of perturbed genes were overlapped between American (AA) and Caucasian American (CA) patients with prostate cancer. Our study indicates that identifying gene expression and/or epigenetic differences between TdECs and NdECs may provide us with new anti-angiogenic targets. Future studies will be required to further characterize the isolated ECs and determine the biological features that can be exploited in the prognosis and therapy of prostate cancer.
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Affiliation(s)
- Wei Luo
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York
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23
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Urbanelli L, Magini A, Ercolani L, Sagini K, Polchi A, Tancini B, Brozzi A, Armeni T, Principato G, Emiliani C. Oncogenic H-Ras up-regulates acid β-hexosaminidase by a mechanism dependent on the autophagy regulator TFEB. PLoS One 2014; 9:e89485. [PMID: 24586816 PMCID: PMC3933543 DOI: 10.1371/journal.pone.0089485] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022] Open
Abstract
The expression of constitutively active H-RasV12 oncogene has been described to induce proliferative arrest and premature senescence in many cell models. There are a number of studies indicating an association between senescence and lysosomal enzyme alterations, e.g. lysosomal β-galactosidase is the most widely used biomarker to detect senescence in cultured cells and we previously reported that H-RasV12 up-regulates lysosomal glycohydrolases enzymatic activity in human fibroblasts. Here we investigated the molecular mechanisms underlying lysosomal glycohydrolase β-hexosaminidase up-regulation in human fibroblasts expressing the constitutively active H-RasV12. We demonstrated that H-Ras activation increases β-hexosaminidase expression and secretion by a Raf/extracellular signal-regulated protein kinase dependent pathway, through a mechanism that relies on the activity of the transcription factor EB (TFEB). Because of the pivotal role of TFEB in the regulation of lysosomal system biogenesis and function, our results suggest that this could be a general mechanism to enhance lysosomal enzymes activity during oncogene-induced senescence.
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Affiliation(s)
- Lorena Urbanelli
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
- * E-mail: (CE); (LU)
| | - Alessandro Magini
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
- Department of Medical and Biological Sciences (DSMB), University of Udine, Udine, Italy
| | - Luisa Ercolani
- Department of Clinical Sciences, Section of Biochemistry, Biology and Physics, Marche Polytechnic University, Ancona, Italy
| | - Krizia Sagini
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
| | - Alice Polchi
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
| | - Brunella Tancini
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
| | - Alessandro Brozzi
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
- Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, Perugia, Italy
| | - Tatiana Armeni
- Department of Clinical Sciences, Section of Biochemistry, Biology and Physics, Marche Polytechnic University, Ancona, Italy
| | - Giovanni Principato
- Department of Clinical Sciences, Section of Biochemistry, Biology and Physics, Marche Polytechnic University, Ancona, Italy
| | - Carla Emiliani
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
- Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, Perugia, Italy
- * E-mail: (CE); (LU)
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24
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Aird KM, Zhang R. Nucleotide metabolism, oncogene-induced senescence and cancer. Cancer Lett 2014; 356:204-10. [PMID: 24486217 DOI: 10.1016/j.canlet.2014.01.017] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/06/2014] [Accepted: 01/22/2014] [Indexed: 01/28/2023]
Abstract
Senescence is defined as a stable cell growth arrest. Oncogene-induced senescence (OIS) occurs when an activated oncogene is expressed in a normal cell. OIS acts as a bona fide tumor suppressor mechanism by driving stable growth arrest of cancer progenitor cells harboring the initial oncogenic hit. OIS is often characterized by aberrant DNA replication and the associated DNA damage response. Nucleotides, in particular deoxyribonucleotide triphosphates (dNTPs), are necessary for both DNA replication and repair. Imbalanced dNTP pools play a role in a number of human diseases, including during the early stages of cancer development. This review will highlight what is currently known about the role of decreased nucleotide metabolism in OIS, how nucleotide metabolism leads to transformation and tumor progression, and how this pathway can be targeted as a cancer therapeutic by inducing senescence of cancer cells.
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Affiliation(s)
- Katherine M Aird
- Gene Expression and Regulation Program, The Wistar Institute Cancer Center, The Wistar Institute, Philadelphia, PA 19104, United States
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute Cancer Center, The Wistar Institute, Philadelphia, PA 19104, United States.
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25
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Aird KM, Li H, Xin F, Konstantinopoulos PA, Zhang R. Identification of ribonucleotide reductase M2 as a potential target for pro-senescence therapy in epithelial ovarian cancer. Cell Cycle 2013; 13:199-207. [PMID: 24200970 DOI: 10.4161/cc.26953] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is the leading cause of gynecological-related cancer deaths in the United States. There is, therefore, an urgent need to develop novel therapeutic strategies for this devastating disease. Cellular senescence is a state of stable cell growth arrest that acts as an important tumor suppression mechanism. Ribonucleotide reductase M2 (RRM2) plays a key role in regulating the senescence-associated cell growth arrest by controlling biogenesis of 2'-deoxyribonucleoside 5'-triphosphates (dNTPs). The role of RRM2 in EOC remains poorly understood. Here we show that RRM2 is expressed at higher levels in EOCs compared with either normal ovarian surface epithelium (P<0.001) or fallopian tube epithelium (P<0.001). RRM2 expression significantly correlates with the expression of Ki67, a marker of cell proliferation (P<0.001). Moreover, RRM2 expression positively correlates with tumor grade and stage, and high RRM2 expression independently predicts a shorter overall survival in EOC patients (P<0.001). To delineate the functional role of RRM2 in EOC, we knocked down RRM2 expression in a panel of EOC cell lines. Knockdown of RRM2 expression inhibits the growth of human EOC cells. Mechanistically, RRM2 knockdown triggers cellular senescence in these cells. Notably, this correlates with the induction of the DNA damage response, a known mediator of cellular senescence. These data suggest that targeting RRM2 in EOCs by suppressing its activity is a novel pro-senescence therapeutic strategy that has the potential to improve survival of EOC patients.
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Affiliation(s)
- Katherine M Aird
- Gene Expression and Regulation Program; The Wistar Institute Cancer Center; The Wistar Institute; Philadelphia, PA USA
| | - Hua Li
- Gene Expression and Regulation Program; The Wistar Institute Cancer Center; The Wistar Institute; Philadelphia, PA USA
| | - Frances Xin
- Cell and Molecular Biology Graduate Program; School of Medicine; The University of Pennsylvania; Philadelphia, PA USA
| | - Panagiotis A Konstantinopoulos
- Medical Gynecological Oncology Program; Dana Farber Cancer Institute; Harvard Medical School; Harvard University; Boston, MA USA
| | - Rugang Zhang
- Gene Expression and Regulation Program; The Wistar Institute Cancer Center; The Wistar Institute; Philadelphia, PA USA
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26
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Fritz A, Sinha S, Marella N, Berezney R. Alterations in replication timing of cancer-related genes in malignant human breast cancer cells. J Cell Biochem 2013; 114:1074-83. [PMID: 23161755 DOI: 10.1002/jcb.24447] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 01/13/2023]
Abstract
The replication timing of nine genes commonly involved in cancer was investigated in the MCF10 cell lines for human breast cancer progression. Six of these nine genes are part of a constellation of tumor suppressor genes that play a major role in familial human breast cancer (TP53, ATM, PTEN, CHK2, BRCA1, and BRCA2). Three other genes are involved in a large number of human cancers including breast as either tumor suppressors (RB1 and RAD51) or as an oncogene (cMYC). Five of these nine genes (TP53, RAD51, ATM, PTEN, and cMYC) show significant differences (P < 0.05) in replication timing between MCF10A normal human breast cells and the corresponding malignant MCF10CA1a cells. These differences are specific to the malignant state of the MCF10CA1a cells since there were no significant differences in the replication timing of these genes between normal MCF10A cells and the non-malignant cancer MCF10AT1 cells. Microarray analysis further demonstrated that three of these five genes (TP53, RAD51, and cMYC) showed significant changes in gene expression (≥2-fold) between normal and malignant cells. Our findings demonstrate an alteration in the replication timing of a small subset of cancer-related genes in malignant breast cancer cells. These alterations partially correlate with the major transcriptional changes characteristic of the malignant state in these cells.
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Affiliation(s)
- Andrew Fritz
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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27
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Rahman MA, Amin AR, Wang D, Koenig L, Nannapaneni S, Chen Z, Wang Z, Sica G, Deng X, Chen Z(G, Shin DM. RRM2 regulates Bcl-2 in head and neck and lung cancers: a potential target for cancer therapy. Clin Cancer Res 2013; 19:3416-28. [PMID: 23719266 PMCID: PMC3747783 DOI: 10.1158/1078-0432.ccr-13-0073] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Ribonucleotide reductase subunit M2 (RRM2) plays an active role in tumor progression. Recently, we reported that depletion of RRM2 by systemic delivery of a nanoparticle carrying RRM2-specific siRNA suppresses head and neck tumor growth. The aim of this study is to clarify the underlying mechanism by which RRM2 depletion inhibits tumor growth. EXPERIMENTAL DESIGN siRNA-mediated gene silencing was carried out to downregulate RRM2. Immunoblotting, reverse-transcriptase PCR, confocal microscopy, tissue fractionation, gene overexpression and knockdown were employed to analyze critical apoptosis signaling. Conventional immunohistochemistry and quantum dot-based immunofluorescence were applied to detect RRM2 and Bcl2 expression and localization in tissue samples from patients and mice. RESULTS Knockdown of RRM2 led to apoptosis through the intrinsic pathway in head and neck squamous cell carcinoma (HNSCC) and non-small cell lung cancer (NSCLC) cell lines. We showed that Bcl-2 is a key determinant controlling apoptosis, both in vitro and in vivo, and that RRM2 depletion significantly reduces Bcl-2 protein expression. We observed that RRM2 regulates Bcl-2 protein stability, with RRM2 suppression leading to increased Bcl-2 degradation, and identified their colocalization in HNSCC and NSCLC cells. In a total of 50 specimens each from patients with HNSCC and NSCLC, we identified the colocalization of Bcl-2 and RRM2 and found a significant positive correlation between their expression in HNSCC (R = 0.98; P < 0.0001) and NSCLC (R = 0.92; P < 0.0001) tumor tissues. CONCLUSIONS Our novel findings add to the knowledge of RRM2 in regulating expression of the antiapoptotic protein Bcl-2 and reveal a critical link between RRM2 and Bcl-2 in apoptosis signaling.
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Affiliation(s)
- Mohammad Aminur Rahman
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - A.R.M. Ruhul Amin
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Dongsheng Wang
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Lydia Koenig
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Sreenivas Nannapaneni
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Zhengjia Chen
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Zhibo Wang
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Gabriel Sica
- Department of Pathology, Emory University, Atlanta, GA, USA
| | - Xingming Deng
- Department of Radiation Oncology, Emory University, Atlanta, GA, USA
| | - Zhuo (Georgia) Chen
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Dong M. Shin
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
- Corresponding Author: Dong M. Shin, Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA 30322. Phone: 1-404-778-2980, Fax: 1-404-778-5520.
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Soto-Rifo R, Ohlmann T. The role of the DEAD-box RNA helicase DDX3 in mRNA metabolism. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:369-85. [PMID: 23606618 DOI: 10.1002/wrna.1165] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
DDX3 belongs to the DEAD-box proteins, a large family of ATP-dependent RNA helicases that participate in all aspects of RNA metabolism. Human DDX3 is a component of several messenger ribonucleoproteins that are found in the spliceosome, the export and the translation initiation machineries but also in different cytoplasmic mRNA granules. DDX3 has been involved in several cellular processes such as cell cycle progression, apoptosis, cancer, innate immune response, and also as a host factor for viral replication. Interestingly, not all these functions require the catalytic activities of DDX3 and thus, the precise roles of this apparently multifaceted protein remain largely obscure. The aim of this review is to provide a rapid and critical overview of the structure and functions of DDX3 with a particular emphasis on its role during mRNA metabolism.
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Affiliation(s)
- Ricardo Soto-Rifo
- Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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