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Du W, Chen W, Shu Z, Xiang D, Bi K, Lu Y, Zhang X, Li L, Diao H. Identification of prognostic biomarkers of hepatocellular carcinoma via long noncoding RNA expression and copy number alterations. Epigenomics 2020; 12:1303-1315. [PMID: 32772564 DOI: 10.2217/epi-2019-0385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study aimed to identify long noncoding RNAs (lncRNAs) with potential to be prognostic biomarkers of hepatocellular carcinoma (HCC) by analyzing copy number alterations (CNAs). Methods: RNA Sequencing data of 369 HCC patients was downloaded from The Cancer Genome Atlas database and analyzed with a series of systematic bioinformatics methods. Results: LncRNA-CNA association analysis revealed that many lncRNAs were located in sites frequently amplified or deleted. Three upregulated lncRNAs (LINC00689, SNHG20 and MAFG-AS1) with copy amplification and one downregulated lncRNA TMEM220-AS1 with copy deletion were associated with poor prognosis of HCC. Conclusion: This study reveals that differentially expressed lncRNAs correlate with CNAs in HCC. Moreover, the differentially expressed lncRNAs and their copy amplification/deletions could be promising prognostic biomarkers of HCC.
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Affiliation(s)
- Weibo Du
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Wenbiao Chen
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Zheyue Shu
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, 310000, China
| | - Dairong Xiang
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Kefan Bi
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Yingfeng Lu
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Xujun Zhang
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
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Assessment of the clinical relevance of 17q25.3 copy number and three-dimensional telomere organization in non-small lung cancer patients. J Cancer Res Clin Oncol 2015; 142:749-56. [DOI: 10.1007/s00432-015-2080-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
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Agell L, Hernández S, Nonell L, Lorenzo M, Puigdecanet E, de Muga S, Juanpere N, Bermudo R, Fernández PL, Lorente JA, Serrano S, Lloreta J. A 12-gene expression signature is associated with aggressive histological in prostate cancer: SEC14L1 and TCEB1 genes are potential markers of progression. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 181:1585-94. [PMID: 23083832 DOI: 10.1016/j.ajpath.2012.08.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 07/24/2012] [Accepted: 08/01/2012] [Indexed: 01/08/2023]
Abstract
The main challenge for clinical management of prostate cancer is to distinguish tumors that will progress faster and will show a higher tendency to recur from the more indolent ones. We have compared expression profiles of 18 prostate cancer samples (seven with a Gleason score of 6, eight with a Gleason score of 7, and three with a Gleason score of ≥8) and five nonneoplastic prostate samples, using the Affymetrix Human Array GeneChip Exon 1.0 ST. Microarray analysis revealed 99 genes showing statistically significant differences among tumors with Gleason scores of 6, 7, and ≥8. In addition, mRNA expression of 29 selected genes was analyzed by real-time quantitative RT-PCR with microfluidic cards in an extended series of 30 prostate tumors. Of the 29 genes, 18 (62%) were independently confirmed in the extended series by quantitative RT-PCR: 14 were up-regulated and 4 were down-regulated in tumors with a higher Gleason score. Twelve of these genes were differentially expressed in tumors with a Gleason score of 6 to 7 versus ≥8. Finally, IHC validation of the protein levels of two genes from the 12-gene signature (SEC14L1 and TCEB1) showed strong protein expression levels of both genes, which were statistically associated with a high combined Gleason score, advanced stage, and prostate-specific antigen progression. This set of genes may contribute to a better understanding of the molecular basis of prostate cancer. TCEB1 and SELC14L1 are good candidate markers for predicting prognosis and progression of prostate cancer.
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Affiliation(s)
- Laia Agell
- Department of Pathology, Hospital del Mar-Mar Health Park, Barcelona, Spain
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Massoner P, Kugler KG, Unterberger K, Kuner R, Mueller LAJ, Fälth M, Schäfer G, Seifarth C, Ecker S, Verdorfer I, Graber A, Sültmann H, Klocker H. Characterization of transcriptional changes in ERG rearrangement-positive prostate cancer identifies the regulation of metabolic sensors such as neuropeptide Y. PLoS One 2013; 8:e55207. [PMID: 23390522 PMCID: PMC3563644 DOI: 10.1371/journal.pone.0055207] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022] Open
Abstract
ERG gene rearrangements are found in about one half of all prostate cancers. Functional analyses do not fully explain the selective pressure causing ERG rearrangement during the development of prostate cancer. To identify transcriptional changes in prostate cancer, including tumors with ERG gene rearrangements, we performed a meta-analysis on published gene expression data followed by validations on mRNA and protein levels as well as first functional investigations. Eight expression studies (n = 561) on human prostate tissues were included in the meta-analysis. Transcriptional changes between prostate cancer and non-cancerous prostate, as well as ERG rearrangement-positive (ERG+) and ERG rearrangement-negative (ERG−) prostate cancer, were analyzed. Detailed results can be accessed through an online database. We validated our meta-analysis using data from our own independent microarray study (n = 57). 84% and 49% (fold-change>2 and >1.5, respectively) of all transcriptional changes between ERG+ and ERG− prostate cancer determined by meta-analysis were verified in the validation study. Selected targets were confirmed by immunohistochemistry: NPY and PLA2G7 (up-regulated in ERG+ cancers), and AZGP1 and TFF3 (down-regulated in ERG+ cancers). First functional investigations for one of the most prominent ERG rearrangement-associated genes - neuropeptide Y (NPY) - revealed increased glucose uptake in vitro indicating the potential role of NPY in regulating cellular metabolism. In summary, we found robust population-independent transcriptional changes in prostate cancer and first signs of ERG rearrangements inducing metabolic changes in cancer cells by activating major metabolic signaling molecules like NPY. Our study indicates that metabolic changes possibly contribute to the selective pressure favoring ERG rearrangements in prostate cancer.
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Affiliation(s)
- Petra Massoner
- Division of Experimental Urology, Department of Urology, Innsbruck Medical University, Innsbruck, Austria
- Oncotyrol, Center for Personalized Cancer Medicine GmbH, Innsbruck, Austria
- * E-mail: (PM); (HK)
| | - Karl G. Kugler
- Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Hall in Tirol, Austria
| | - Karin Unterberger
- Oncotyrol, Center for Personalized Cancer Medicine GmbH, Innsbruck, Austria
| | - Ruprecht Kuner
- Unit Cancer Genome Research, Division of Molecular Genetics, German Cancer Research Center and National Center of Tumor Diseases, Heidelberg, Germany
| | - Laurin A. J. Mueller
- Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Hall in Tirol, Austria
| | - Maria Fälth
- Unit Cancer Genome Research, Division of Molecular Genetics, German Cancer Research Center and National Center of Tumor Diseases, Heidelberg, Germany
| | - Georg Schäfer
- Division of Experimental Urology, Department of Urology, Innsbruck Medical University, Innsbruck, Austria
| | - Christof Seifarth
- Division of Experimental Urology, Department of Urology, Innsbruck Medical University, Innsbruck, Austria
| | - Simone Ecker
- Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Hall in Tirol, Austria
| | - Irmgard Verdorfer
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Armin Graber
- Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Hall in Tirol, Austria
| | - Holger Sültmann
- Unit Cancer Genome Research, Division of Molecular Genetics, German Cancer Research Center and National Center of Tumor Diseases, Heidelberg, Germany
| | - Helmut Klocker
- Division of Experimental Urology, Department of Urology, Innsbruck Medical University, Innsbruck, Austria
- Oncotyrol, Center for Personalized Cancer Medicine GmbH, Innsbruck, Austria
- * E-mail: (PM); (HK)
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Bermudo R, Abia D, Mozos A, García-Cruz E, Alcaraz A, Ortiz AR, Thomson TM, Fernández PL. Highly sensitive molecular diagnosis of prostate cancer using surplus material washed off from biopsy needles. Br J Cancer 2011; 105:1600-7. [PMID: 22009027 PMCID: PMC3242534 DOI: 10.1038/bjc.2011.435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Introduction: Currently, final diagnosis of prostate cancer (PCa) is based on histopathological analysis of needle biopsies, but this process often bears uncertainties due to small sample size, tumour focality and pathologist's subjective assessment. Methods: Prostate cancer diagnostic signatures were generated by applying linear discriminant analysis to microarray and real-time RT–PCR (qRT–PCR) data from normal and tumoural prostate tissue samples. Additionally, after removal of biopsy tissues, material washed off from transrectal biopsy needles was used for molecular profiling and discriminant analysis. Results: Linear discriminant analysis applied to microarray data for a set of 318 genes differentially expressed between non-tumoural and tumoural prostate samples produced 26 gene signatures, which classified the 84 samples used with 100% accuracy. To identify signatures potentially useful for the diagnosis of prostate biopsies, surplus material washed off from routine biopsy needles from 53 patients was used to generate qRT–PCR data for a subset of 11 genes. This analysis identified a six-gene signature that correctly assigned the biopsies as benign or tumoural in 92.6% of the cases, with 88.8% sensitivity and 96.1% specificity. Conclusion: Surplus material from prostate needle biopsies can be used for minimal-size gene signature analysis for sensitive and accurate discrimination between non-tumoural and tumoural prostates, without interference with current diagnostic procedures. This approach could be a useful adjunct to current procedures in PCa diagnosis.
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Affiliation(s)
- R Bermudo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, c. Villarroel 170, 08036, Barcelona, Spain
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Fang M, Shen Z, Huang S, Zhao L, Chen S, Mak TW, Wang X. The ER UDPase ENTPD5 promotes protein N-glycosylation, the Warburg effect, and proliferation in the PTEN pathway. Cell 2010; 143:711-24. [PMID: 21074248 DOI: 10.1016/j.cell.2010.10.010] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 09/10/2010] [Accepted: 10/07/2010] [Indexed: 12/19/2022]
Abstract
PI3K and PTEN lipid phosphatase control the level of cellular phosphatidylinositol (3,4,5)-trisphosphate, an activator of AKT kinases that promotes cell growth and survival. Mutations activating AKT are commonly observed in human cancers. We report here that ENTPD5, an endoplasmic reticulum (ER) enzyme, is upregulated in cell lines and primary human tumor samples with active AKT. ENTPD5 hydrolyzes UDP to UMP to promote protein N-glycosylation and folding in ER. Knockdown of ENTPD5 in PTEN null cells causes ER stress and loss of growth factor receptors. ENTPD5, together with cytidine monophosphate kinase-1 and adenylate kinase-1, constitute an ATP hydrolysis cycle that converts ATP to AMP, resulting in a compensatory increase in aerobic glycolysis known as the Warburg effect. The growth of PTEN null cells is inhibited both in vitro and in mouse xenograft tumor models. ENTPD5 is therefore an integral part of the PI3K/PTEN regulatory loop and a potential target for anticancer therapy.
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Affiliation(s)
- Min Fang
- Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 75390, USA
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Bermudo R, Abia D, Benitez D, Carrió A, Vilella R, Ortiz ÁR, Thomson TM, Fernández PL. Discovery of genomic alterations through coregulation analysis of closely linked genes: a frequent gain in 17q25.3 in prostate cancer. Ann N Y Acad Sci 2010; 1210:17-24. [DOI: 10.1111/j.1749-6632.2010.05780.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abia D, Bastolla U, Chacón P, Fábrega C, Gago F, Morreale A, Tramontano A. In memoriam. Proteins 2010; 78:iii-viii. [DOI: 10.1002/prot.22660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Timofeeva OA, Zhang X, Ressom HW, Varghese RS, Kallakury BVS, Wang K, Ji Y, Cheema A, Jung M, Brown ML, Rhim JS, Dritschilo A. Enhanced expression of SOS1 is detected in prostate cancer epithelial cells from African-American men. Int J Oncol 2009; 35:751-60. [PMID: 19724911 PMCID: PMC3727633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
African-American (AA) men experience an increased risk of developing prostate cancers as well as increased mortality following treatment as compared to European-American (EA) men. The aim of our study was to identify biological factors with the potential to predispose AA men to prostate tumor progression and metastasis. To identify cancer-specific gene expression patterns in AA men, we established primary prostate cancer epithelial cells from 14 AA and 13 EA men. High-throughput microarrays were used to investigate differences in global gene expression comparing the two groups. Quantitative RT-PCR and immunohistochemistry validated mRNA and protein expression levels. RNAi knockdowns provided support for biological significance for the identified genes in prostate cancer cells. Son of sevenless homolog 1 (SOS1) was overexpressed in AA male-derived primary prostate cancer epithelial cells. Depletion of SOS1 in PC3 and DU145 prostate cancer cells resulted in decreased capacities for cell proliferation, migration and invasion, at least partially through inhibition of extracellular signal-regulated kinase 1 and 2. Tissue microarray analyses of SOS1 expression in prostate carcinomas correlated with Gleason's grades of tumors, consistent with a possible role in prostate cancer progression. Investigation of prostate cancer-derived epithelial cells has led to identification of SOS1 as a potential candidate biomarker and molecular therapeutic target in prostate cancer in AA men, consistent with the hypothesis that a biological basis exists for prostate cancer aggressiveness in AA men.
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Affiliation(s)
- Olga A. Timofeeva
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
| | - Xueping Zhang
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
| | - Habtom W. Ressom
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
| | - Rency S. Varghese
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
| | - Bhaskar VS. Kallakury
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
| | - Kan Wang
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
| | - Youngmi Ji
- Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Amrita Cheema
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
| | - Mira Jung
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
| | - Milton L. Brown
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
| | - Johng S. Rhim
- Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Anatoly Dritschilo
- Vincent T. Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057
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