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Krushkal J, Zhao Y, Roney K, Zhu W, Brooks A, Wilsker D, Parchment RE, McShane LM, Doroshow JH. Association of changes in expression of HDAC and SIRT genes after drug treatment with cancer cell line sensitivity to kinase inhibitors. Epigenetics 2024; 19:2309824. [PMID: 38369747 PMCID: PMC10878021 DOI: 10.1080/15592294.2024.2309824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/14/2024] [Indexed: 02/20/2024] Open
Abstract
Histone deacetylases (HDACs) and sirtuins (SIRTs) are important epigenetic regulators of cancer pathways. There is a limited understanding of how transcriptional regulation of their genes is affected by chemotherapeutic agents, and how such transcriptional changes affect tumour sensitivity to drug treatment. We investigated the concerted transcriptional response of HDAC and SIRT genes to 15 approved antitumor agents in the NCI-60 cancer cell line panel. Antitumor agents with diverse mechanisms of action induced upregulation or downregulation of multiple HDAC and SIRT genes. HDAC5 was upregulated by dasatinib and erlotinib in the majority of the cell lines. Tumour cell line sensitivity to kinase inhibitors was associated with upregulation of HDAC5, HDAC1, and several SIRT genes. We confirmed changes in HDAC and SIRT expression in independent datasets. We also experimentally validated the upregulation of HDAC5 mRNA and protein expression by dasatinib in the highly sensitive IGROV1 cell line. HDAC5 was not upregulated in the UACC-257 cell line resistant to dasatinib. The effects of cancer drug treatment on expression of HDAC and SIRT genes may influence chemosensitivity and may need to be considered during chemotherapy.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Kyle Roney
- Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC, USA
| | - Weimin Zhu
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Alan Brooks
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Deborah Wilsker
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ralph E. Parchment
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa M. McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - James H. Doroshow
- Division of Cancer Treatment and Diagnosis and Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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2
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Wang TN, Yang PJ, Tseng YT, Tsai YS, Kuo PL, Chiu CC, Liang SS, Hsieh TH, Hou MF, Tsai EM. Visceral obesity and cell cycle pathways serve as links in the association between bisphenol A exposure and breast cancer. Oncol Lett 2020; 20:33-42. [PMID: 32565931 PMCID: PMC7285711 DOI: 10.3892/ol.2020.11553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/16/2018] [Indexed: 11/05/2022] Open
Abstract
It has been identified that bisphenol A (BPA) exposure causes developmental toxicity in breast cells. However, the exact molecular mechanisms underlying the association between exposure to BPA and breast cancer remain unclear. The aim of the present study was to investigate the BPA-regulated signaling pathways associated with the aggressiveness and the development of breast cancer. Microarray technology and functional gene set analyses were used to evaluate BPA and breast cancer-associated biomarkers and pathways in a discovery-driven manner. Using individual dataset analyses, it was indicated that two BPA-associated gene sets, the visceral obesity pathway, involved in visceral fat deposits and the metabolic syndrome, and the cell cycle pathway, involved in cyclins and cell cycle regulation, were significantly associated with a high grade of aggressiveness and the development of estrogen receptor (ER)-positive breast cancer (between P<0.05 and 0.0001). The pooled analysis indicated that the most significant pathway was G1/S checkpoint regulation, and the cyclin and cell cycle regulation pathway for BPA-associated ER-positive cancer. Cancer cell signaling pathways were associated with healthy breast cells developing into breast cancer. The visceral obesity and the cell cycle pathways were indicated to link BPA exposure to breast cancer. The results of the present study demonstrate a significant association between breast cancer and BPA-regulated gene pathways.
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Affiliation(s)
- Tsu-Nai Wang
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C.,Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Pei-Jing Yang
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Yu-Ting Tseng
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Yi-Shan Tsai
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Po-Lin Kuo
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C.,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Chien-Chih Chiu
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C.,Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Shih-Shin Liang
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C.,Institute of Biomedical Science, College of Science, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan, R.O.C
| | - Tsung-Hua Hsieh
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan, R.O.C
| | - Ming-Feng Hou
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C.,Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan, R.O.C.,Department of Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan, R.O.C.,Department of Surgery, Kaohsiung Municipal Siaogang Hospital, Kaohsiung 81267, Taiwan, R.O.C.,Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 30010, Taiwan, R.O.C
| | - Eing-Mei Tsai
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C.,Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan, R.O.C.,Center for Research Resources and Development, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan, R.O.C.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
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3
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Meng X, Fang E, Zhao X, Feng J. Identification of prognostic long noncoding RNAs associated with spontaneous regression of neuroblastoma. Cancer Med 2020; 9:3800-3815. [PMID: 32216054 PMCID: PMC7286466 DOI: 10.1002/cam4.3022] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/25/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background The association between long noncoding RNAs (lncRNAs) and spontaneous regression of neuroblastoma (NB) has rarely been investigated and remains unknown. Objective To identify prognostic lncRNAs involved in the spontaneous regression of NB. Methods Differential expression analyses were performed between those samples with an outcome of death in stage 4 NB group and those samples with an outcome of survival in stage 4S NB group in two independent public datasets, respectively. Univariate Cox proportional hazard regression survival analysis was performed in each of the entire cohort to identify those lncRNAs significantly associated with overall survival (OS). Those lncRNAs independently associated with OS were then identified by multivariate Cox survival analysis and used to construct an lncRNA risk score. Results A total of 20 differentially expressed and survival‐related lncRNAs were identified sharing between the two independent cohorts. The expression of each of these 20 lncRNAs was significantly correlated with the expression of NTRK1, which is a well‐known factor involved in NB spontaneous regression. Four lncRNAs (LNC00839, FIRRE, LOC283177, and LOC101928100) were identified to be significantly associated with survival independent with each other and a four‐lncRNA signature risk score was constructed. Patients with high lncRNA signature risk score had a significantly poorer OS and event‐free survival than those with low lncRNA signature risk score. The four‐lncRNA signature has a good performance in predicting survival independent with MYCN amplification (nonamplified vs amplified), age status (<18 months vs ≥18 months), risk status (low risk vs high risk), and International Neuroblastoma Staging System (INSS) stage (INSS 1/2/3/4S vs INSS 4). Conclusions We identified 20 survival‐related lncRNAs that might be associated with the spontaneous regression of NB and developed a four‐lncRNA signature risk score. The four‐lncRNA signature is an independent prognostic factor for survival of NB patients.
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Affiliation(s)
- Xinyao Meng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Erhu Fang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Zhao
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiexiong Feng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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4
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Palmisano A, Krushkal J, Li MC, Fang J, Sonkin D, Wright G, Yee L, Zhao Y, McShane L. Bioinformatics Tools and Resources for Cancer Immunotherapy Study. Methods Mol Biol 2020; 2055:649-678. [PMID: 31502173 DOI: 10.1007/978-1-4939-9773-2_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In recent years, cancer immunotherapy has emerged as a highly promising approach to treat patients with cancer, as the patient's own immune system is harnessed to attack cancer cells. However, the application of these approaches is still limited to a minority of patients with cancer and it is difficult to predict which patients will derive the greatest clinical benefit.One of the challenges faced by the biomedical community in the search of more effective biomarkers is the fact that translational research efforts involve collecting and accessing data at many different levels: from the type of material examined (e.g., cell line, animal models, clinical samples) to multiple data type (e.g., pharmacodynamic markers, genetic sequencing data) to the scale of a study (e.g., small preclinical study, moderate retrospective study on stored specimen sets, clinical trials with large cohorts).This chapter reviews several publicly available bioinformatics tools and data resources for high throughput molecular analyses applied to a range of data types, including those generated from microarray, whole-exome sequencing (WES), RNA-seq, DNA copy number, and DNA methylation assays, that are extensively used for integrative multidimensional data analysis and visualization.
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Affiliation(s)
- Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ming-Chung Li
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianwen Fang
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George Wright
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura Yee
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lisa McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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5
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Evolving Genomics of Pulmonary Fibrosis. Respir Med 2019. [DOI: 10.1007/978-3-319-99975-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Rossow L, Veitl S, Vorlová S, Wax JK, Kuhn AE, Maltzahn V, Upcin B, Karl F, Hoffmann H, Gätzner S, Kallius M, Nandigama R, Scheld D, Irmak S, Herterich S, Zernecke A, Ergün S, Henke E. LOX-catalyzed collagen stabilization is a proximal cause for intrinsic resistance to chemotherapy. Oncogene 2018; 37:4921-4940. [PMID: 29780168 PMCID: PMC6127085 DOI: 10.1038/s41388-018-0320-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/23/2018] [Accepted: 04/13/2018] [Indexed: 12/18/2022]
Abstract
The potential of altering the tumor ECM to improve drug response remains fairly unexplored. To identify targets for modification of the ECM aiming to improve drug response and overcome resistance, we analyzed expression data sets from pre-treatment patient cohorts. Cross-evaluation identified a subset of chemoresistant tumors characterized by increased expression of collagens and collagen-stabilizing enzymes. We demonstrate that strong collagen expression and stabilization sets off a vicious circle of self-propagating hypoxia, malignant signaling, and aberrant angiogenesis that can be broken by an appropriate auxiliary intervention: Interfering with collagen stabilization by inhibition of lysyl oxidases significantly enhanced response to chemotherapy in various tumor models, even in metastatic disease. Inhibition of collagen stabilization by itself can reduce or enhance tumor growth depending on the tumor type. The mechanistical basis for this behavior is the dependence of the individual tumor on nutritional supply on one hand and on high tissue stiffness for FAK signaling on the other.
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Affiliation(s)
- Leonie Rossow
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany
| | - Simona Veitl
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany
| | - Sandra Vorlová
- Institute of Experimental Biomedicine, Universitätsklinikum Würzburg, Josef-Schneider-Strasse 2, 97082, Würzburg, Germany
| | - Jacqueline K Wax
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany
| | - Anja E Kuhn
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany
| | - Verena Maltzahn
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany
| | - Berin Upcin
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany.,School of Health Sciences, Bilgi University, 34440, Beyoğlu İstanbul, Turkey
| | - Franziska Karl
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany.,Institute of Experimental Biomedicine, Universitätsklinikum Würzburg, Josef-Schneider-Strasse 2, 97082, Würzburg, Germany
| | - Helene Hoffmann
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany.,Institute of Experimental Biomedicine, Universitätsklinikum Würzburg, Josef-Schneider-Strasse 2, 97082, Würzburg, Germany
| | - Sabine Gätzner
- Institute of Tissue Engineering, Universität Würzburg, Roentgenring 11, 97070, Würzburg, Germany
| | - Matthias Kallius
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany.,Graduate School of Life Science, Josef-Schneider-Strasse 2, 97082, Würzburg, Germany
| | - Rajender Nandigama
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany
| | - Daniela Scheld
- Zentrallabor, Universitätsklinikum Würzburg, Josef-Schneider-Strasse 2, 97082, Würzburg, Germany
| | - Ster Irmak
- School of Health Sciences, Bilgi University, 34440, Beyoğlu İstanbul, Turkey
| | - Sabine Herterich
- Zentrallabor, Universitätsklinikum Würzburg, Josef-Schneider-Strasse 2, 97082, Würzburg, Germany
| | - Alma Zernecke
- Institute of Experimental Biomedicine, Universitätsklinikum Würzburg, Josef-Schneider-Strasse 2, 97082, Würzburg, Germany
| | - Süleyman Ergün
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany
| | - Erik Henke
- Institute of Anatomy and Cell Biology II, Universität Würzburg, Koellikerstrasse 6, 97070, Würzburg, Germany. .,Graduate School of Life Science, Josef-Schneider-Strasse 2, 97082, Würzburg, Germany.
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7
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Teicher BA, Silvers T, Selby M, Delosh R, Laudeman J, Ogle C, Reinhart R, Parchment R, Krushkal J, Sonkin D, Rubinstein L, Morris J, Evans D. Small cell lung carcinoma cell line screen of etoposide/carboplatin plus a third agent. Cancer Med 2017; 6:1952-1964. [PMID: 28766886 PMCID: PMC5548882 DOI: 10.1002/cam4.1131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 12/28/2022] Open
Abstract
The SCLC combination screen examined a 9-point concentration response of 180 third agents, alone and in combination with etoposide/carboplatin. The predominant effect of adding a third agent to etoposide/carboplatin was additivity. Less than additive effects occurred frequently in SCLC lines sensitive to etoposide/carboplatin. In SCLC lines with little or no response to etoposide/carboplatin, greater than additive SCLC killing occurred over the entire spectrum of SCLC lines but never occurred in all SCLC lines. Exposing SCLC lines to tubulin-targeted agents (paclitaxel or vinorelbine) simultaneously with etoposide/carboplatin resulted primarily in less than additive cell killing. As single agents, nuclear kinase inhibitors including Aurora kinase inhibitors, Kinesin Spindle Protein/EG5 inhibitors, and Polo-like kinase-1 inhibitors were potent cytotoxic agents in SCLC lines; however, simultaneous exposure of the SCLC lines to these agents along with etoposide/carboplatin, generally, resulted in less than additive cell killing. Several classes of agents enhanced the cytotoxicity of etoposide/carboplatin toward the SCLC lines. Exposure of the SCLC lines to the MDM2 inhibitor JNJ-27291199 produced enhanced killing in 80% of the SCLC lines. Chk-1 inhibitors such as rabusertib increased the cytotoxicity of etoposide/carboplatin to the SCLC lines in an additive to greater than additive manner. The combination of GSK-3β inhibitor LY-2090314 with etoposide/carboplatin increased killing in approximately 40% of the SCLC lines. Exposure to the BET bromodomain inhibitor MK-8628 increased the SCLC cell killing by etoposide/carboplatin in 20-25% of the SCLC lines. Only 10-15% of the SCLC lines had an increased response to etoposide/carboplatin when simultaneously exposed to the PARP inhibitor talazoparib.
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Affiliation(s)
- Beverly A. Teicher
- Developmental Therapeutics ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteBethesdaMaryland20892
| | - Thomas Silvers
- Molecular Pharmacology GroupLeidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickMaryland21702
| | - Michael Selby
- Molecular Pharmacology GroupLeidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickMaryland21702
| | - Rene Delosh
- Molecular Pharmacology GroupLeidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickMaryland21702
| | - Julie Laudeman
- Molecular Pharmacology GroupLeidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickMaryland21702
| | - Chad Ogle
- Molecular Pharmacology GroupLeidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickMaryland21702
| | - Russell Reinhart
- Molecular Pharmacology GroupLeidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickMaryland21702
| | - Ralph Parchment
- Molecular Pharmacology GroupLeidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickMaryland21702
| | - Julia Krushkal
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisBethesdaMaryland20892
| | - Dmitriy Sonkin
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisBethesdaMaryland20892
| | - Larry Rubinstein
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisBethesdaMaryland20892
| | - Joel Morris
- Developmental Therapeutics ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteBethesdaMaryland20892
| | - David Evans
- Molecular Pharmacology GroupLeidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickMaryland21702
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8
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González-Prendes R, Quintanilla R, Amills M. Investigating the genetic regulation of the expression of 63 lipid metabolism genes in the pig skeletal muscle. Anim Genet 2017; 48:606-610. [DOI: 10.1111/age.12586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2017] [Indexed: 01/22/2023]
Affiliation(s)
- R. González-Prendes
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus de la Universitat Autònoma de Barcelona Bellaterra 08193 Spain
| | - R. Quintanilla
- Animal Breeding and Genetics Program; Institut de Recerca i Tecnologia Agroalimentàries (IRTA); Torre Marimon Caldes de Montbui 08140 Spain
| | - M. Amills
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus de la Universitat Autònoma de Barcelona Bellaterra 08193 Spain
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
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9
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González-Prendes R, Quintanilla R, Cánovas A, Manunza A, Figueiredo Cardoso T, Jordana J, Noguera JL, Pena RN, Amills M. Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits. Sci Rep 2017; 7:39830. [PMID: 28054563 PMCID: PMC5215505 DOI: 10.1038/srep39830] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/29/2016] [Indexed: 12/28/2022] Open
Abstract
Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism.
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Affiliation(s)
- Rayner González-Prendes
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain
| | - Angela Cánovas
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Arianna Manunza
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Tainã Figueiredo Cardoso
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia D. F., Zip Code 70.040-020, Brazil
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - José Luis Noguera
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida - Agrotecnio Center, Lleida 25198, Spain
| | - Marcel Amills
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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10
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Gilabert-Juan J, Sáez AR, Lopez-Campos G, Sebastiá-Ortega N, González-Martínez R, Costa J, Haro JM, Callado LF, Meana JJ, Nacher J, Sanjuán J, Moltó MD. Semaphorin and plexin gene expression is altered in the prefrontal cortex of schizophrenia patients with and without auditory hallucinations. Psychiatry Res 2015; 229:850-7. [PMID: 26243375 DOI: 10.1016/j.psychres.2015.07.074] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 06/24/2015] [Accepted: 07/26/2015] [Indexed: 02/07/2023]
Abstract
Auditory hallucinations (AH) are clinical hallmarks of schizophrenia, however little is known about molecular genetics of these symptoms. In this study, gene expression profiling of postmortem brain samples from prefrontal cortex of schizophrenic patients without AH (SNA), patients with AH (SA) and control subjects were compared. Genome-wide expression analysis was conducted using samples of three individuals of each group and the Affymetrix GeneChip Human-Gene 1.0 ST-Array. This analysis identified the Axon Guidance pathway as one of the most differentially expressed network among SNA, SA and CNT. To confirm the transcriptome results, mRNA level quantification of seventeen genes involved in this pathway was performed in a larger sample. PLXNB1, SEMA3A, SEMA4D and SEM6C were upregulated in SNA or SA patients compared to controls. PLXNA1 and SEMA3D showed down-regulation in their expression in the patient's samples, but differences remained statistically significant between the SNA patients and controls. Differences between SNA and SA were found in PLXNB1 expression which is decreased in SA patients. This study strengthens the contribution of brain plasticity in pathophysiology of schizophrenia and shows that non-hallucinatory patients present more alterations in frontal regions than patients with hallucinations concerning neural plasticity.
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Affiliation(s)
- Javier Gilabert-Juan
- CIBERSAM, Spain; Departamento de Genética, Facultad de Biología, Universitat de València, INCLIVA, Valencia, Spain; Unidad de Neurobiología y Programa de Neurociencias Básicas y Aplicadas, Departamento de Biología Celular, Universitat de València, INCLIVA, Valencia, Spain
| | - Ana Rosa Sáez
- Departamento de Genética, Facultad de Biología, Universitat de València, INCLIVA, Valencia, Spain
| | | | - Noelia Sebastiá-Ortega
- Departamento de Genética, Facultad de Biología, Universitat de València, INCLIVA, Valencia, Spain
| | - Rocio González-Martínez
- Departamento de Genética, Facultad de Biología, Universitat de València, INCLIVA, Valencia, Spain; Unidad de Neurobiología y Programa de Neurociencias Básicas y Aplicadas, Departamento de Biología Celular, Universitat de València, INCLIVA, Valencia, Spain
| | - Juan Costa
- Parc Sanitari Sant Joan de Déu, Fundació Sant Joan de Deu, Barcelona, Spain
| | - Josep María Haro
- CIBERSAM, Spain; Parc Sanitari Sant Joan de Déu, Fundació Sant Joan de Deu, Barcelona, Spain
| | - Luis F Callado
- CIBERSAM, Spain; Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Spain
| | - J Javier Meana
- CIBERSAM, Spain; Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Spain; BioCruces Health Research Institute, Spain
| | - Juán Nacher
- CIBERSAM, Spain; Unidad de Neurobiología y Programa de Neurociencias Básicas y Aplicadas, Departamento de Biología Celular, Universitat de València, INCLIVA, Valencia, Spain
| | - Julio Sanjuán
- CIBERSAM, Spain; Hospital Clínico de Valencia, Universitat de València INCLIVA, Valencia, Spain
| | - María Dolores Moltó
- CIBERSAM, Spain; Departamento de Genética, Facultad de Biología, Universitat de València, INCLIVA, Valencia, Spain.
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11
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Yang WS, Chadalapaka G, Cho SG, Lee SO, Jin UH, Jutooru I, Choi K, Leung YK, Ho SM, Safe S, Kim K. The transcriptional repressor ZBTB4 regulates EZH2 through a MicroRNA-ZBTB4-specificity protein signaling axis. Neoplasia 2015; 16:1059-69. [PMID: 25499219 PMCID: PMC4309261 DOI: 10.1016/j.neo.2014.09.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/22/2014] [Accepted: 09/29/2014] [Indexed: 10/28/2022] Open
Abstract
ZBTB4 is a transcriptional repressor and examination of publically-available microarray data sets demonstrated an inverse relationship in the prognostic value and expression of ZBTB4 and the histone methyltransferase EZH2 in tumors from breast cancer patients. The possibility of functional interactions between EZH2 and ZBTB4 was investigated in breast cancer cells and the results showed that EZH2 is directly suppressed by ZBTB4 which in turn is regulated (suppressed) by miR-106b and other paralogues from the miR-17-92, miR-106b-25 and miR-106a-363 clusters that are highly expressed in breast and other tumors. ZBTB4 also acts a suppressor of specificity protein (Sp) transcription factors Sp1, Sp3 and Sp4, and RNA interference studies show that Sp proteins are required for EZH2 expression. The prediction analysis results from breast cancer patient array data sets confirm an association of Sp1-dependent EZH2 gene signature with decreased survival of breast cancer patients. Disruption of oncogenic miR-ZBTB4 signaling axis by anticancer agent such as betulinic acid that induce down-regulation of Sp proteins in breast cancer cells resulted in inhibition of tumor growth and colonization of breast cancer cells in a mouse model. Thus, EZH2 is reciprocally regulated by a novel signaling network consisting of Sp proteins, oncogenic miRs and ZBTB4, and modulation of this gene network is a novel therapeutic approach for treatment of breast cancer and possibly other cancers.
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Affiliation(s)
- Won Seok Yang
- Department of Environmental Health, University of Cincinnati, College of Medicine, 3223 Eden Ave., Cincinnati, OH 45267
| | - Gayathri Chadalapaka
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, 4466 Texas A&M University, College Station, TX 77843
| | - Sung-Gook Cho
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, 1 Hoegi, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Syng-Ook Lee
- Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 W. Holcombe Blvd., Houston, TX 77030
| | - Un-Ho Jin
- Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 W. Holcombe Blvd., Houston, TX 77030
| | - Indira Jutooru
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, 4466 Texas A&M University, College Station, TX 77843
| | - Kwangmin Choi
- Division of Experimental Biology and Cancer Biology, Cincinnati Children's Hospital medical Center, Cincinnati, OH 45229
| | - Yuet-Kin Leung
- Department of Environmental Health, University of Cincinnati, College of Medicine, 3223 Eden Ave., Cincinnati, OH 45267
| | - Shuk-Mei Ho
- Department of Environmental Health, University of Cincinnati, College of Medicine, 3223 Eden Ave., Cincinnati, OH 45267
| | - Stephen Safe
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, 4466 Texas A&M University, College Station, TX 77843; Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 W. Holcombe Blvd., Houston, TX 77030
| | - Kyounghyun Kim
- Department of Environmental Health, University of Cincinnati, College of Medicine, 3223 Eden Ave., Cincinnati, OH 45267
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12
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Ellsworth DL, Mamula KA, Blackburn HL, McDyer FA, Jellema GL, van Laar R, Costantino NS, Engler RJM, Vernalis MN. Importance of substantial weight loss for altering gene expression during cardiovascular lifestyle modification. Obesity (Silver Spring) 2015; 23:1312-9. [PMID: 25960328 DOI: 10.1002/oby.21079] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/13/2015] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To examine relationships between weight loss through changes in lifestyle and peripheral blood gene expression profiles. METHODS A prospective nonrandomized trial was conducted over 1 year in participants undergoing intensive lifestyle modification to reverse or stabilize progression of coronary artery disease. Cardiovascular risk factors, inflammatory biomarkers, and gene expression as a function of weight loss were assessed in 89 lifestyle participants and 71 retrospectively matched controls undergoing usual care. RESULTS Substantial weight loss (-15.2 ± 3.8%) in lifestyle participants (n = 33) was associated with improvement in selected cardiovascular risk factors and significant changes in peripheral blood gene expression from pre- to post-intervention: 132 unique genes showed significant expression changes (false discovery rate corrected P-value <0.05 and fold-change ≥1.4). Altered molecular pathways were related to immune function and inflammatory responses involving endothelial activation. In contrast, participants losing minimal weight (-3.1 ± 2.5%, n = 32) showed only minor changes in cardiovascular risk factors and markers of inflammation and no changes in gene expression compared to non intervention controls after 1 year. CONCLUSIONS Weight loss (≥10%) during lifestyle modification is associated with down-regulation of genetic pathways governing interactions between circulating immune cells and the vascular endothelium and may be required to successfully reduce CVD risk.
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Affiliation(s)
- Darrell L Ellsworth
- Integrative Cardiac Health Program, Windber Research Institute, Windber, Pennsylvania, USA
| | - Kimberly A Mamula
- Integrative Cardiac Health Program, Windber Research Institute, Windber, Pennsylvania, USA
| | - Heather L Blackburn
- Integrative Cardiac Health Program, Windber Research Institute, Windber, Pennsylvania, USA
| | | | | | - Ryan van Laar
- Bioinformatics Department, ChipDX LLC, New York, New York, USA
| | - Nicholas S Costantino
- Integrative Cardiac Health Program, Windber Research Institute, Windber, Pennsylvania, USA
| | - Renata J M Engler
- Integrative Cardiac Health Program, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Marina N Vernalis
- Integrative Cardiac Health Program, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
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13
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Park D, Lee SC, Park JW, Cho SY, Kim HK. Overexpression of miR-17 in gastric cancer is correlated with proliferation-associated oncogene amplification. Pathol Int 2015; 64:309-14. [PMID: 25047501 DOI: 10.1111/pin.12178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 05/20/2014] [Indexed: 12/14/2022]
Abstract
The molecular mechanism underlying microRNA (miR)-17 overexpression has not been clearly evaluated in gastric cancer. We aimed to evaluate the functional roles of miR-17 in gastric cancer and test its viability as a therapeutic target. We conducted comparative genomic hybridization and expression array analyses on human gastric cancer tissue samples, as well as evaluating the functional roles of miR-17 in gastric cancer cell lines and transgenic mice. miR-17 overexpression in gastric cancer patients was associated with copy number gain of proliferation-associated oncogenes such as MYC, CCNE1, ERBB2, and FGFR2. Copy number gain of MIR17HG gene (13q31.3) was rare, with an overall frequency of 2% in gastric cancers (1 of 51). miR-17 knockdown suppressed the monolayer and anchorage-independent growth of FGFR2-amplified KATO-III gastric cancer cells. mir-17-92 TG/TG mice overexpressing the mir-17-92 cluster under the villin promoter developed spontaneous benign tumors in the intestinal tract (log-rank P for tumor-free survival = 0.069). Taken together, miR-17 overexpression in gastric cancer was rarely associated with MIR17HG gene amplification, but correlated with proliferation-associated oncogene amplification. Therefore, miR-17-targeting approach may benefit patients with gastric cancers harboring proliferation-associated oncogene amplification.
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14
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Forster L, McCooke J, Bellgard M, Joske D, Finlayson J, Ghassemifar R. Differential gene expression analysis in early and late erythroid progenitor cells in β-thalassaemia. Br J Haematol 2015; 170:257-67. [DOI: 10.1111/bjh.13432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/19/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Luke Forster
- School of Pathology and Laboratory Medicine; University of Western Australia; Nedlands WA Australia
| | - John McCooke
- Centre for Comparative Genomics; Murdoch University; Murdoch WA Australia
| | - Matthew Bellgard
- Centre for Comparative Genomics; Murdoch University; Murdoch WA Australia
| | - David Joske
- Department of Haematology; PathWest Laboratory Medicine; Queen Elizabeth II Medical Centre; Nedlands WA Australia
| | - Jill Finlayson
- School of Pathology and Laboratory Medicine; University of Western Australia; Nedlands WA Australia
- Department of Haematology; PathWest Laboratory Medicine; Queen Elizabeth II Medical Centre; Nedlands WA Australia
| | - Reza Ghassemifar
- School of Pathology and Laboratory Medicine; University of Western Australia; Nedlands WA Australia
- Department of Haematology; PathWest Laboratory Medicine; Queen Elizabeth II Medical Centre; Nedlands WA Australia
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15
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Kim BY, Choi DW, Woo SR, Park ER, Lee JG, Kim SH, Koo I, Park SH, Han CJ, Kim SB, Yeom YI, Yang SJ, Yu A, Lee JW, Jang JJ, Cho MH, Jeon WK, Park YN, Suh KS, Lee KH. Recurrence-associated pathways in hepatitis B virus-positive hepatocellular carcinoma. BMC Genomics 2015; 16:279. [PMID: 25888140 PMCID: PMC4448317 DOI: 10.1186/s12864-015-1472-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 03/20/2015] [Indexed: 02/01/2023] Open
Abstract
Background Despite the recent identification of several prognostic gene signatures, the lack of common genes among experimental cohorts has posed a considerable challenge in uncovering the molecular basis underlying hepatocellular carcinoma (HCC) recurrence for application in clinical purposes. To overcome the limitations of individual gene-based analysis, we applied a pathway-based approach for analysis of HCC recurrence. Results By implementing a permutation-based semi-supervised principal component analysis algorithm using the optimal principal component, we selected sixty-four pathways associated with hepatitis B virus (HBV)-positive HCC recurrence (p < 0.01), from our microarray dataset composed of 142 HBV-positive HCCs. In relation to the public HBV- and public hepatitis C virus (HCV)-positive HCC datasets, we detected 46 (71.9%) and 18 (28.1%) common recurrence-associated pathways, respectively. However, overlap of recurrence-associated genes between datasets was rare, further supporting the utility of the pathway-based approach for recurrence analysis between different HCC datasets. Non-supervised clustering of the 64 recurrence-associated pathways facilitated the classification of HCC patients into high- and low-risk subgroups, based on risk of recurrence (p < 0.0001). The pathways identified were additionally successfully applied to discriminate subgroups depending on recurrence risk within the public HCC datasets. Through multivariate analysis, these recurrence-associated pathways were identified as an independent prognostic factor (p < 0.0001) along with tumor number, tumor size and Edmondson’s grade. Moreover, the pathway-based approach had a clinical advantage in terms of discriminating the high-risk subgroup (N = 12) among patients (N = 26) with small HCC (<3 cm). Conclusions Using pathway-based analysis, we successfully identified the pathways involved in recurrence of HBV-positive HCC that may be effectively used as prognostic markers. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1472-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bu-Yeo Kim
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, Korea.
| | - Dong Wook Choi
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, 215-4 Gongneung-dong, Nowon-ku, Seoul, 139-706, Korea. .,Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Seon Rang Woo
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, 215-4 Gongneung-dong, Nowon-ku, Seoul, 139-706, Korea.
| | - Eun-Ran Park
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, 215-4 Gongneung-dong, Nowon-ku, Seoul, 139-706, Korea. .,Department of Pathology and BK 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
| | - Je-Geun Lee
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, 215-4 Gongneung-dong, Nowon-ku, Seoul, 139-706, Korea.
| | - Su-Hyeon Kim
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, 215-4 Gongneung-dong, Nowon-ku, Seoul, 139-706, Korea.
| | - Imhoi Koo
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, USA.
| | - Sun-Hoo Park
- Department of Pathology, Korea Institute of Radiological and Medical Sciences, Seoul, Korea.
| | - Chul Ju Han
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, 215-4 Gongneung-dong, Nowon-ku, Seoul, 139-706, Korea. .,Department of Internal Medicine, Korea Institute of Radiological and Medical Sciences, Seoul, Korea.
| | - Sang Bum Kim
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, 215-4 Gongneung-dong, Nowon-ku, Seoul, 139-706, Korea. .,Department of Surgery, Korea Institute of Radiological and Medical Sciences, Seoul, Korea.
| | - Young Il Yeom
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
| | - Suk-Jin Yang
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
| | - Ami Yu
- Department of Statistics, Korea University, Seoul, Korea. .,Korean Medicine Clinical Trial Center, Kyung Hee University Oriental Medicine Hospital, Seoul, Korea.
| | - Jae Won Lee
- Department of Statistics, Korea University, Seoul, Korea.
| | - Ja June Jang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.
| | - Myung-Haing Cho
- Laboratory of Toxicology and Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Korea.
| | - Won Kyung Jeon
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, Korea.
| | - Young Nyun Park
- Department of Pathology and BK 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
| | - Kyung-Suk Suh
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea.
| | - Kee-Ho Lee
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, 215-4 Gongneung-dong, Nowon-ku, Seoul, 139-706, Korea. .,Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, Korea.
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16
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Rajagopalan A, Schweizer N, Nordenankar K, Nilufar Jahan S, Emilsson L, Wallén-Mackenzie Å. Reduced gene expression levels of Munc13-1 and additional components of the presynaptic exocytosis machinery upon conditional targeting of Vglut2 in the adolescent mouse. Synapse 2014; 68:624-633. [PMID: 25139798 DOI: 10.1002/syn.21776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 07/04/2014] [Accepted: 07/11/2014] [Indexed: 11/06/2022]
Abstract
Presynaptic proteins orchestrate an intricate interplay of dynamic interactions in order to regulate quantal exocytosis of transmitter-filled vesicles, and their dysregulation might cause neurological and neuropsychiatric dysfunction. Mice carrying a spatiotemporal restriction in the expression of the Vesicular glutamate transporter 2 (Vglut2; aka Slc17a6) in the cortex, amygdala and hippocampal subiculum from the third postnatal week show a strong anxiolytic phenotype and certain behavioral correlates of schizophrenia. To further understand the molecular consequences of this targeted deletion of Vglut2, we performed an unbiased microarray analysis comparing gene expression levels in the subiculum of these conditional Vglut2 knockout mice (Vglut2f/f;CamKII cKO) to those in control littermates. Expression of Unc13C (Munc13-3), a member of the Unc/Munc family, previously shown to be important for glutamatergic transmission, was identified to be significantly down-regulated. Subsequent analysis by quantitative RT-PCR revealed a 50% down-regulation of Munc 13-1, the gene encoding the Unc/Munc subtype described as an essential component in the majority of glutamtergic synapses in the hippocampus. Genes encoding additional components of the presynaptic machinery were also found regulated, including Rab3A, RIM1α, as well as Syntaxin1 and Synaptobrevin. Altered expression levels of these genes were further found in the amygdala and in the retrosplenial group of the cortex, additional regions in which Vglut2 was conditionally targeted. These findings suggest that expression levels of Vglut2 might be important for the maintenance of gene expression in the presynaptic machinery in the adult mouse brain. Synapse 68:624-633, 2014. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Aparna Rajagopalan
- Department of Neuroscience, Units of Functional Neurobiology and Developmental Genetics, Uppsala University, S-752 37, Uppsala, Sweden
| | - Nadine Schweizer
- Department of Neuroscience, Units of Functional Neurobiology and Developmental Genetics, Uppsala University, S-752 37, Uppsala, Sweden
| | - Karin Nordenankar
- Department of Neuroscience, Units of Functional Neurobiology and Developmental Genetics, Uppsala University, S-752 37, Uppsala, Sweden
| | - Sultana Nilufar Jahan
- Department of Neuroscience, Units of Functional Neurobiology and Developmental Genetics, Uppsala University, S-752 37, Uppsala, Sweden
| | - Lina Emilsson
- Department of Neuroscience, Units of Functional Neurobiology and Developmental Genetics, Uppsala University, S-752 37, Uppsala, Sweden.,Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, S-752 36, Uppsala, Sweden
| | - Åsa Wallén-Mackenzie
- Department of Neuroscience, Units of Functional Neurobiology and Developmental Genetics, Uppsala University, S-752 37, Uppsala, Sweden
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Manunza A, Casellas J, Quintanilla R, González-Prendes R, Pena RN, Tibau J, Mercadé A, Castelló A, Aznárez N, Hernández-Sánchez J, Amills M. A genome-wide association analysis for porcine serum lipid traits reveals the existence of age-specific genetic determinants. BMC Genomics 2014; 15:758. [PMID: 25189197 PMCID: PMC4164741 DOI: 10.1186/1471-2164-15-758] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 07/25/2014] [Indexed: 01/07/2023] Open
Abstract
Background The genetic determinism of blood lipid concentrations, the main risk factor for atherosclerosis, is practically unknown in species other than human and mouse. Even in model organisms, little is known about how the genetic determinants of lipid traits are modulated by age-specific factors. To gain new insights into this issue, we have carried out a genome-wide association study (GWAS) for cholesterol (CHOL), triglyceride (TRIG) and low (LDL) and high (HDL) density lipoprotein concentrations measured in Duroc pigs at two time points (45 and 190 days). Results Analysis of data with mixed-model methods (EMMAX, GEMMA, GenABEL) and PLINK showed a low positional concordance between trait-associated regions (TARs) for serum lipids at 45 and 190 days. Besides, the proportion of phenotypic variance explained by SNPs at these two time points was also substantially different. The four analyses consistently detected two regions on SSC3 (124 Mb, CHOL and LDL at 190 days) and SSC6 (135 Mb, CHOL and TRIG at 190 days) with highly significant effects on the porcine blood lipid profile. Moreover, we have found that SNP variation within SSC3, SSC6, SSC10, SSC13 and SSC16 TARs is associated with the expression of several genes mapping to other chromosomes and related to lipid metabolism. Conclusions Our data demonstrate that the effects of genomic determinants influencing lipid concentrations in pigs, as well as the amount of phenotypic variance they explain, are influenced by age-related factors. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-758) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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18
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TPX2 expression is associated with cell proliferation and patient outcome in esophageal squamous cell carcinoma. J Gastroenterol 2014; 49:1231-40. [PMID: 23963785 DOI: 10.1007/s00535-013-0870-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/02/2013] [Indexed: 02/04/2023]
Abstract
BACKGROUND The molecular and genetic changes underlying esophageal squamous cell carcinoma (ESCC) tumor formation and rapid progression are poorly understood. Using high-throughput data analysis, we examined molecular changes involved in ESCC pathogenesis and investigated their clinical relevance. METHODS Five independent microarray datasets were examined for differentially expressed genes and pathways. For validation, mRNA expression in tumor and matched normal tissues from 16 ESCC cases was examined by cDNA microarray, and protein expression in 97 ESCC specimens was investigated using immunohistochemical stains. The association between clinicopathological parameters and the expression of Aurora kinase A (Aurora-A) and TPX2 was analyzed. The impact of TPX2 expression was also assessed in ESCC cancer cells. RESULTS AURKA and TPX2, members of the "Role of Ran in mitotic spindle regulation" pathway, were selected for further investigation. Verification by cDNA microarray showed that both genes were overexpressed in tumor tissues, and immunohistochemical staining showed Aurora-A and TPX2 expression in 88.4 and 90.6 % of ESCC specimens, respectively. High TPX2 expression was a significant prognosticator for overall and disease-free survival in univariate analysis and remained an independent prognostic factor in multivariate analysis (HR 1.802, p = 0.037). TPX2 knockdown clones showed inhibited cellular proliferation in growth curve studies and formed fewer colonies in the clonogenic assay. CONCLUSIONS Using bioinformatics resources, which were validated by microarray analysis and immunohistochemistry stains, and manipulation of TPX2 expression in ESCC cell lines, we demonstrated that TPX2 expression is associated with cell proliferation and poor prognosis among patients with resected ESCC.
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19
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Genetic and cytokine changes associated with symptomatic stages of CLL. Leuk Res 2014; 38:1097-101. [PMID: 25063525 DOI: 10.1016/j.leukres.2014.05.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 05/21/2014] [Accepted: 05/25/2014] [Indexed: 01/23/2023]
Abstract
The pathogenesis and drug resistance of symptomatic CLL patients involves genetic changes associated with the CLL clone as well as changes within the microenvironment. To further understand these processes, we compared early stage CLL to symptomatic late stage using gene expression and serum cytokine profiling to gain insight of the genetic and microenvironment changes associated with the most severe form of the disease. Patients were classified into low stage (Rai stage 0/I/II) and high stage (Rai stage III/IV). Gene expression profiles were obtained on pretreatment samples using the HG-U133A 2.0 Affymetrix platform. A comparison of low versus high stage CLL revealed a set of 21 genes differentially expressed genes. 15 genes were up regulated in the high stage compared to low stage while 6 genes were down regulated. Analysis of GO molecular function revealed 9 of 21 genes were involved in transcription factor activity. Serum cytokine profiles showed six cytokines to be significantly different in high stage patients. Two chemokines, SDF-1/CXCL12 and uPAR known to be involved in stem cell mobilization and homing were increased in serum of high stage patients. This study has identified therapeutic targets for symptomatic CLL patients.
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20
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Óvilo C, Benítez R, Fernández A, Núñez Y, Ayuso M, Fernández AI, Rodríguez C, Isabel B, Rey AI, López-Bote C, Silió L. Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics. BMC Genomics 2014; 15:413. [PMID: 24885501 PMCID: PMC4070551 DOI: 10.1186/1471-2164-15-413] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/27/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in piglets of both genetic types, in order to identify genes, pathways and regulatory factors responsible for their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DU×IB) were generated. Piglets (14 from each genetic type) were slaughtered at weaning (28 days) and longissimus dorsi was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays. RESULTS Loin muscle chemical composition showed significant differences between genetic types in intramuscular fat content (6.1% vs. 4.3% in IB and DUxIB animals, respectively, P = 0.009) and in saturated (P = 0.019) and monounsaturated fatty acid proportions (P = 0.044). The statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR < 0.10), 102 upregulated in IB and 154 upregulated in DU×IB. Transcript differences were validated for a subset of DE genes by qPCR. We observed alteration in biological functions related to extracellular matrix function and organization, cellular adhesion, muscle growth, lipid metabolism and proteolysis. Candidate genes with known effects on muscle growth were found among the DE genes upregulated in DU×IB. Genes related to lipid metabolism and proteolysis were found among those upregulated in IB. Regulatory factors (RF) potentially involved in the expression differences were identified by calculating the regulatory impact factors. Twenty-nine RF were found, some of them with known relationship with tissue development (MSTN, SIX4, IRX3), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these RF and DE genes show relevant differences between genetic types. CONCLUSION These results provide valuable information about genetic mechanisms determining the phenotypic differences on growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. Transcription factors and regulatory mechanisms are proposed for these altered biological functions.
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Affiliation(s)
- Cristina Óvilo
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Rita Benítez
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Almudena Fernández
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Yolanda Núñez
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Miriam Ayuso
- />Dpto Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | | | - Carmen Rodríguez
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Beatriz Isabel
- />Dpto Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | - Ana Isabel Rey
- />Dpto Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | | | - Luis Silió
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
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Óvilo C, Benítez R, Fernández A, Isabel B, Núñez Y, Fernández AI, Rodríguez C, Daza A, Silió L, López-Bote C. Dietary energy source largely affects tissue fatty acid composition but has minor influence on gene transcription in Iberian pigs. J Anim Sci 2014; 92:939-54. [PMID: 24492573 DOI: 10.2527/jas.2013-6988] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A trial was performed to compare the effects of different dietary sources of MUFA on the fatty acid (FA) composition, lipid metabolism, and gene transcription in different tissues of Iberian pigs. Twenty-seven Iberian male pigs of 28 kg live weight (LW) were divided in 2 groups and fed with 1 of 2 isocaloric diets: a standard diet with carbohydrates as energy source (CH) and a diet enriched with high-oleic sunflower oil (HO). Ham adipose tissue was sampled by biopsy at 44 and 70 kg LW. At 110 kg LW pigs were slaughtered and backfat, loin, and liver tissues were sampled. Animals of the HO group showed higher MUFA content and lower SFA in all the analyzed tissues (P < 0.001). These main effects were established early during the treatment and increased only slightly along time. Small diet effects were also detected on PUFA, which showed differences according to sampling time, tissue, and lipid fraction. Effects of diet on gene expression were explored with a combined approach analyzing adipose tissue transcriptome and quantifying the expression of a panel of key genes implicated in lipogenesis and lipid metabolism processes in backfat, muscle, and liver. Backfat transcriptome showed small effects of diet on gene expression, in number and magnitude. According to the posterior probabilities (PP) of the probe-specific expression differences between dietary groups (PP < 0.01), 37 genes were considered differentially expressed (DE). Gene ontology allowed relating them with several biological functions including lipid metabolic processes. Quantitative PCR confirmed several DE genes in adipose tissue (RXRG, LEP, and ME1; P < 0.0001, P < 0.05, and P < 0.0001, respectively), but no DE gene was found in loin or liver tissues. Joint results agree with a metabolic adjustment of adipose tissue FA levels by the subtle effect of the diet on the regulation of several lipid metabolism pathways, mainly FA oxidation and prostanoid synthesis, with LEP, RXRG, and PTGS2 genes playing mayor roles.
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Affiliation(s)
- C Óvilo
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
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Hsu PK, Kao HL, Chen HY, Yen CC, Wu YC, Hsu WH, Chou TY. Loss of CRNN expression is associated with advanced tumor stage and poor survival in patients with esophageal squamous cell carcinoma. J Thorac Cardiovasc Surg 2013; 147:1612-1618.e4. [PMID: 24263008 DOI: 10.1016/j.jtcvs.2013.09.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/16/2013] [Accepted: 09/30/2013] [Indexed: 11/17/2022]
Abstract
OBJECTIVE CRNN gene expression is downregulated in esophageal squamous cell carcinoma (ESCC), although its clinical implications in esophageal cancer remain unclear. METHODS We performed integrated microarray analysis and identified the CRNN gene as 1 of the major downregulated genes in ESCC. CRNN downregulation was validated at the nucleic acid level in 16 ESCC cases using complementary DNA microarray and at the protein level by immunohistochemical stains in an additional 220 ESCC cases. The clinicopathologic relevance and prognostic significance of CRNN expression in ESCC were explored. RESULTS Downregulated CRNN expression was noted at the messenger RNA and protein levels. Immunohistochemical staining revealed negative and positive CRNN expression in 171 (77.7%) and 49 (22.3%) patients with ESCC, respectively. Patients with negative CRNN protein expression had an advanced tumor invasion depth (P = .002), advanced nodal involvement (P = .014), and longer tumor length (P = .037). Patients with negative CRNN expression (median survival, 14.0 months; 5-year survival rate, 20.5%) had poorer overall survival than those with positive expression (30.0 months and 40.3%, respectively; P = .006). On multivariate analysis, negative CRNN expression, nodal involvement, and distant metastasis remained significant prognostic factors for poor overall survival (negative vs positive CRNN, hazard ratio, 1.464; P = .047). CONCLUSIONS Our analysis has highlighted the clinical implications of CRNN expression in ESCC. Loss of CRNN expression correlated with advanced tumor length, greater tumor invasion depth, lymph node metastasis, and poor survival in patients with ESCC.
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Affiliation(s)
- Po-Kuei Hsu
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan; National Yang-Ming University School of Medicine, Taipei City, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei City, Taiwan
| | - Hua-Ling Kao
- National Yang-Ming University School of Medicine, Taipei City, Taiwan; Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, Taipei City, Taiwan
| | - Chueh-Chuan Yen
- Division of Hematology and Oncology, Department of Medicine, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Yu-Chung Wu
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan; National Yang-Ming University School of Medicine, Taipei City, Taiwan
| | - Wen-Hu Hsu
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Teh-Ying Chou
- National Yang-Ming University School of Medicine, Taipei City, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei City, Taiwan; Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei City, Taiwan.
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Kim SJ, Sohn I, Do IG, Jung SH, Ko YH, Yoo HY, Paik S, Kim WS. Gene expression profiles for the prediction of progression-free survival in diffuse large B cell lymphoma: results of a DASL assay. Ann Hematol 2013; 93:437-47. [DOI: 10.1007/s00277-013-1884-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 08/14/2013] [Indexed: 11/28/2022]
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Pena RN, Noguera JL, Casellas J, Díaz I, Fernández AI, Folch JM, Ibáñez-Escriche N. Transcriptional analysis of intramuscular fatty acid composition in the longissimus thoracis muscle of Iberian × Landrace back-crossed pigs. Anim Genet 2013; 44:648-60. [PMID: 23826865 DOI: 10.1111/age.12066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2013] [Indexed: 11/29/2022]
Abstract
This study aimed at identifying differential gene expression conditional on the fatty acid profile of the longissimus thoracis (Lt) muscle, a prime cut of economic relevance for fresh and cured pork production. A population of 110 Iberian (25%) × Landrace (75%) back-crossed pigs was used, because these two breeds exhibit extreme profiles of intramuscular saturated fatty acid, monounsaturated fatty acid (MUFA) and polyunsaturated fatty acid (PUFA) contents. Total RNA from Lt muscle was individually hybridized to GeneChip Porcine Genome arrays (Affymetrix). A principal component analysis was performed with data from the 110 animals to select 40 extreme animals based on the total fatty acid profile and the MUFA composition (MAP). Comparison of global transcription levels between extreme fatty acid profile pigs (n = 40) resulted in 219 differentially expressed probes (false discovery rate <0.10). Gene ontology, pathway and network analysis indicated that animals with higher percentages of PUFA exhibit a shift toward a more oxidative muscular metabolism state, with a raise in mitochondria function (PPARGC1A, ATF2), fatty acid uptake and oxidation (FABP5, MGLL). On the other hand, 87 probes were differentially expressed between MUFA composition groups (n = 40; false discovery rate <0.10). In particular, muscles rich in n-7 MUFA expressed higher levels of genes involved in lipid metabolism (GLUL, CRAT, PLA2G15) and lower levels of fatty acid elongation genes (ELOVL5). Moreover, the chromosomal position of FABP5, PAQR3, MGLL, PPARGC1A, GLUL and ELOVL5 co-localized with very relevant QTL for fat deposition and composition described in the same resource population. This study represents a complementary approach to identifying genes underlying these QTL effects.
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Affiliation(s)
- R N Pena
- Genètica i Millora Animal, IRTA, 191 Av. Rovira Roure, 25198, Lleida, Spain; Departament de Producció Animal, ETSEA, Universitat de Lleida, 191 Av. Rovira Roure, 25198, Lleida, Spain
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Cánovas A, Varona L, Burgos C, Galve A, Carrodeguas JA, Ibáñez-Escriche N, Martín- Burriel I, López-Buesa P. Early postmortem gene expression and its relationship to composition and quality traits in pig Longissimus dorsi muscle1. J Anim Sci 2012; 90:3325-36. [DOI: 10.2527/jas.2011-4799] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- A. Cánovas
- Universidad de Zaragoza, Departamento de Genética Cuantitativa y Mejora Animal. Facultad de Veterinaria, Miguel Servet 177, 50013 Zaragoza, Spain
| | - L. Varona
- Universidad de Zaragoza, Departamento de Genética Cuantitativa y Mejora Animal. Facultad de Veterinaria, Miguel Servet 177, 50013 Zaragoza, Spain
| | - C. Burgos
- Universidad de Zaragoza, Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Miguel Servet 177, 50013 Zaragoza, Spain
| | - A. Galve
- Universidad de Zaragoza, Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Miguel Servet 177, 50013 Zaragoza, Spain
| | - J. A. Carrodeguas
- Universidad de Zaragoza, Instituto de Biocomputación y Física de Sistemas Complejos, Miguel Servet 177, 50013 Zaragoza, Spain
| | - N. Ibáñez-Escriche
- Institut de Recerca i Tecnologia Agroalimentària. Area de Genètica i Millora Animal, Rovira Roure, 191, 25198 Lleida, Spain
| | - I. Martín- Burriel
- Universidad de Zaragoza, Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Miguel Servet 177, 50013 Zaragoza, Spain
| | - P. López-Buesa
- Universidad de Zaragoza, Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Miguel Servet 177, 50013 Zaragoza, Spain
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Bolt AM, Zhao F, Pacheco S, Klimecki WT. Arsenite-induced autophagy is associated with proteotoxicity in human lymphoblastoid cells. Toxicol Appl Pharmacol 2012; 264:255-61. [PMID: 22959463 DOI: 10.1016/j.taap.2012.08.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/18/2012] [Accepted: 08/07/2012] [Indexed: 11/19/2022]
Abstract
Epidemiological studies of arsenic-exposed populations have provided evidence that arsenic exposure in humans is associated with immunosuppression. Previously, we have reported that arsenite-induced toxicity is associated with the induction of autophagy in human lymphoblastoid cell lines (LCL). Autophagy is a cellular process that functions in the degradation of damaged cellular components, including protein aggregates formed by misfolded or damaged proteins. Accumulation of misfolded or damaged proteins in the endoplasmic reticulum (ER) lumen causes ER stress and activates the unfolded protein response (UPR). In an effort to investigate the mechanism of autophagy induction by arsenite in the LCL model, we examined the potential contribution of ER stress and activation of the UPR. LCL exposed to sodium arsenite for 8-days induced expression of UPR-activated genes, including CHOP and GRP78, at the RNA and the protein level. Evidence for activation of the three arms of the UPR was observed. The arsenite-induced activation of the UPR was associated with an accumulation of protein aggregates containing p62 and LC3, proteins with established roles in the sequestration and autophagic clearance of protein aggregates. Taken together, these data provide evidence that arsenite-induced autophagy is associated with the generation of ER stress, activation of the UPR, and formation of protein aggregates that may be targeted to the lysosome for degradation.
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Affiliation(s)
- Alicia M Bolt
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
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Cánovas A, Pena RN, Gallardo D, Ramírez O, Amills M, Quintanilla R. Segregation of regulatory polymorphisms with effects on the gluteus medius transcriptome in a purebred pig population. PLoS One 2012; 7:e35583. [PMID: 22545120 PMCID: PMC3335821 DOI: 10.1371/journal.pone.0035583] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/19/2012] [Indexed: 01/21/2023] Open
Abstract
Background The main goal of the present study was to analyse the genetic architecture of mRNA expression in muscle, a tissue with an outmost economic importance for pig breeders. Previous studies have used F2 crosses to detect porcine expression QTL (eQTL), so they contributed with data that mostly represents the between-breed component of eQTL variation. Herewith, we have analysed eQTL segregation in an outbred Duroc population using two groups of animals with divergent fatness profiles. This approach is particularly suitable to analyse the within-breed component of eQTL variation, with a special emphasis on loci involved in lipid metabolism. Methodology/Principal Findings GeneChip Porcine Genome arrays (Affymetrix) were used to determine the mRNA expression levels of gluteus medius samples from 105 Duroc barrows. A whole-genome eQTL scan was carried out with a panel of 116 microsatellites. Results allowed us to detect 613 genome-wide significant eQTL unevenly distributed across the pig genome. A clear predominance of trans- over cis-eQTL, was observed. Moreover, 11 trans-regulatory hotspots affecting the expression levels of four to 16 genes were identified. A Gene Ontology study showed that regulatory polymorphisms affected the expression of muscle development and lipid metabolism genes. A number of positional concordances between eQTL and lipid trait QTL were also found, whereas limited evidence of a linear relationship between muscle fat deposition and mRNA levels of eQTL regulated genes was obtained. Conclusions/Significance Our data provide substantial evidence that there is a remarkable amount of within-breed genetic variation affecting muscle mRNA expression. Most of this variation acts in trans and influences biological processes related with muscle development, lipid deposition and energy balance. The identification of the underlying causal mutations and the ascertainment of their effects on phenotypes would allow gaining a fundamental perspective about how complex traits are built at the molecular level.
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Affiliation(s)
| | - Ramona N. Pena
- IRTA, Genètica i Millora Animal, Lleida, Spain
- * E-mail: (RQ); (RP)
| | - David Gallardo
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Oscar Ramírez
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Marcel Amills
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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Ben-Hamo R, Efroni S. Biomarker robustness reveals the PDGF network as driving disease outcome in ovarian cancer patients in multiple studies. BMC SYSTEMS BIOLOGY 2012; 6:3. [PMID: 22236809 PMCID: PMC3298526 DOI: 10.1186/1752-0509-6-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 01/11/2012] [Indexed: 12/27/2022]
Abstract
Background Ovarian cancer causes more deaths than any other gynecological cancer. Identifying the molecular mechanisms that drive disease progress in ovarian cancer is a critical step in providing therapeutics, improving diagnostics, and affiliating clinical behavior with disease etiology. Identification of molecular interactions that stratify prognosis is key in facilitating a clinical-molecular perspective. Results The Cancer Genome Atlas has recently made available the molecular characteristics of more than 500 patients. We used the TCGA multi-analysis study, and two additional datasets and a set of computational algorithms that we developed. The computational algorithms are based on methods that identify network alterations and quantify network behavior through gene expression. We identify a network biomarker that significantly stratifies survival rates in ovarian cancer patients. Interestingly, expression levels of single or sets of genes do not explain the prognostic stratification. The discovered biomarker is composed of the network around the PDGF pathway. The biomarker enables prognosis stratification. Conclusion The work presented here demonstrates, through the power of gene-expression networks, the criticality of the PDGF network in driving disease course. In uncovering the specific interactions within the network, that drive the phenotype, we catalyze targeted treatment, facilitate prognosis and offer a novel perspective into hidden disease heterogeneity.
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Wu MT, Lee TC, Wu IC, Su HJ, Huang JL, Peng CY, Wang W, Chou TY, Lin MY, Lin WY, Huang CT, Pan CH, Ho CK. Whole genome expression in peripheral-blood samples of workers professionally exposed to polycyclic aromatic hydrocarbons. Chem Res Toxicol 2011; 24:1636-43. [PMID: 21854004 DOI: 10.1021/tx200181q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This study aims to examine global gene expression profiles before and after the work-shift among coke-oven workers (COWs). COWs work six consecutive days and then take two days off. Two blood and urine samples in each worker were collected before starting to work after two days off and end-of-shift in the sixth day of work in 2009. Altered gene expressions (ratio of gene expression levels between end-of-shift and preshift work) were performed by a Human OneArray expression system which probes ~30,000-transcription expression profiling of human genes. Sixteen workers, all men, were enrolled in this study. Median urinary 1-hydroxypyrene (1OHP) levels (μmol/mol creatinine) in end-of-shift work were significantly higher than those in preshift work (2.58 vs 0.29, p = 0.0002). Among the 20,341 genes which passed experimental quality control, 26 gene expression changes, 7 positive and 19 negative, were highly correlated with across-the-shift urinary 1OHP levels (end-of-shift-preshift 1OHP) (p-value <0.001). The high and low exposure groups of across-the-shift urinary 1OHP levels dichotomized in ~2.00 μmol/mol creatinine were able to be distinguished by these 26 genes. Some of them are known to be involved in apoptosis, chromosome stability/DNA repair, cell cycle control/tumor suppressor, cell adhesion, development/spermatogenesis, immune function, and neuronal cell function. These findings in COWs will be an ideal model to study the relationship of PAH exposure with acute changes of gene expressions.
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Affiliation(s)
- Ming-Tsang Wu
- Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
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Daves MH, Hilsenbeck SG, Lau CC, Man TK. Meta-analysis of multiple microarray datasets reveals a common gene signature of metastasis in solid tumors. BMC Med Genomics 2011; 4:56. [PMID: 21736749 PMCID: PMC3212952 DOI: 10.1186/1755-8794-4-56] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 07/07/2011] [Indexed: 02/02/2023] Open
Abstract
Background Metastasis is the number one cause of cancer deaths. Expression microarrays have been widely used to study metastasis in various types of cancer. We hypothesize that a meta-analysis of publicly available gene expression datasets in various tumor types can identify a signature of metastasis that is common to multiple tumor types. This common signature of metastasis may help us to understand the shared steps in the metastatic process and identify useful biomarkers that could predict metastatic risk. Methods We identified 18 publicly available gene expression datasets in the Oncomine database comparing distant metastases to primary tumors in various solid tumors which met our eligibility criteria. We performed a meta-analysis using a modified permutation counting method in order to obtain a common gene signature of metastasis. We then validated this signature in independent datasets using gene set expression comparison analysis with the LS-statistic. Results A common metastatic signature of 79 genes was identified in the metastatic lesions compared with primaries with a False Discovery Proportion of less than 0.1. Interestingly, all the genes in the signature, except one, were significantly down-regulated, suggesting that overcoming metastatic suppression may be a key feature common to all metastatic tumors. Pathway analysis of the significant genes showed that the genes were involved in known metastasis-associated pathways, such as integrin signaling, calcium signaling, and VEGF signaling. To validate the signature, we used an additional six expression datasets that were not used in the discovery study. Our results showed that the signature was significantly enriched in four validation sets with p-values less than 0.05. Conclusions We have modified a previously published meta-analysis method and identified a common metastatic signature by comparing primary tumors versus metastases in various tumor types. This approach, as well as the gene signature identified, provides important insights to the common metastatic process and a foundation for future discoveries that could have broad application, such as drug discovery, metastasis prediction, and mechanistic studies.
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Affiliation(s)
- Marla H Daves
- Dan L, Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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Kim HK, Kim J, Korolevich S, Choi IJ, Kim CH, Munroe DJ, Green JE. Distinctions in gastric cancer gene expression signatures derived from laser capture microdissection versus histologic macrodissection. BMC Med Genomics 2011; 4:48. [PMID: 21635755 PMCID: PMC3141377 DOI: 10.1186/1755-8794-4-48] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 06/02/2011] [Indexed: 02/08/2023] Open
Abstract
Background Gastric cancer samples obtained by histologic macrodissection contain a relatively high stromal content that may significantly influence gene expression profiles. Differences between the gene expression signature derived from macrodissected gastric cancer samples and the signature obtained from isolated gastric cancer epithelial cells from the same biopsies using laser-capture microdissection (LCM) were evaluated for their potential experimental biases. Methods RNA was isolated from frozen tissue samples of gastric cancer biopsies from 20 patients using both histologic macrodissection and LCM techniques. RNA from LCM was subject to an additional round of T7 RNA amplification. Expression profiling was performed using Affymetrix HG-U133A arrays. Genes identified in the expression signatures from each tissue processing method were compared to the set of genes contained within chromosomal regions found to harbor copy number aberrations in the tumor samples by array CGH and to proteins previously identified as being overexpressed in gastric cancer. Results Genes shown to have increased copy number in gastric cancer were also found to be overexpressed in samples obtained by macrodissection (LS P value < 10-5), but not in array data generated using microdissection. A set of 58 previously identified genes overexpressed in gastric cancer was also enriched in the gene signature identified by macrodissection (LS P < 10-5), but not in the signature identified by microdissection (LS P = 0.013). In contrast, 66 genes previously reported to be underexpressed in gastric cancer were enriched in the gene signature identified by microdissection (LS P < 10-5), but not in the signature identified by macrodissection (LS P = 0.89). Conclusions The tumor sampling technique biases the microarray results. LCM may be a more sensitive collection and processing method for the identification of potential tumor suppressor gene candidates in gastric cancer using expression profiling.
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A gene expression signature of acquired chemoresistance to cisplatin and fluorouracil combination chemotherapy in gastric cancer patients. PLoS One 2011; 6:e16694. [PMID: 21364753 PMCID: PMC3041770 DOI: 10.1371/journal.pone.0016694] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/24/2010] [Indexed: 12/16/2022] Open
Abstract
Background We initiated a prospective trial to identify transcriptional alterations associated with acquired chemotherapy resistance from pre- and post-biopsy samples from the same patient and uncover potential molecular pathways involved in treatment failure to help guide therapeutic alternatives. Methodology/Principal Findings A prospective, high-throughput transcriptional profiling study was performed using endoscopic biopsy samples from 123 metastatic gastric cancer patients prior to cisplatin and fluorouracil (CF) combination chemotherapy. 22 patients who initially responded to CF were re-biopsied after they developed resistance to CF. An acquired chemotherapy resistance signature was identified by analyzing the gene expression profiles from the matched pre- and post-CF treated samples. The acquired resistance signature was able to segregate a separate cohort of 101 newly-diagnosed gastric cancer patients according to the time to progression after CF. Hierarchical clustering using a 633-gene acquired resistance signature (feature selection at P<0.01) separated the 101 pretreatment patient samples into two groups with significantly different times to progression (2.5 vs. 4.7 months). This 633-gene signature included the upregulation of AKT1, EIF4B, and RPS6 (mTOR pathway), DNA repair and drug metabolism genes, and was enriched for genes overexpressed in embryonic stem cell signatures. A 72-gene acquired resistance signature (a subset of the 633 gene signature also identified in ES cell-related gene sets) was an independent predictor for time to progression (adjusted P = 0.011) and survival (adjusted P = 0.034) of these 101 patients. Conclusion/Significance This signature may offer new insights into identifying new targets and therapies required to overcome the acquired resistance of gastric cancer to CF.
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Cánovas A, Quintanilla R, Amills M, Pena RN. Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits. BMC Genomics 2010; 11:372. [PMID: 20540717 PMCID: PMC2894043 DOI: 10.1186/1471-2164-11-372] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 06/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Selection for increasing intramuscular fat content would definitively improve the palatability and juiciness of pig meat as well as the sensorial and organoleptic properties of cured products. However, evidences obtained in human and model organisms suggest that high levels of intramuscular fat might alter muscle lipid and carbohydrate metabolism. We have analysed this issue by determining the transcriptomic profiles of Duroc pigs with divergent phenotypes for 13 fatness traits. The strong aptitude of Duroc pigs to have high levels of intramuscular fat makes them a valuable model to analyse the mechanisms that regulate muscle lipid metabolism, an issue with evident implications in the elucidation of the genetic basis of human metabolic diseases such as obesity and insulin resistance. RESULTS Muscle gene expression profiles of 68 Duroc pigs belonging to two groups (HIGH and LOW) with extreme phenotypes for lipid deposition and composition traits have been analysed. Microarray and quantitative PCR analysis showed that genes related to fatty acid uptake, lipogenesis and triacylglycerol synthesis were upregulated in the muscle tissue of HIGH pigs, which are fatter and have higher amounts of intramuscular fat than their LOW counterparts. Paradoxically, lipolytic genes also showed increased mRNA levels in the HIGH group suggesting the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Several genes related to the insulin-signalling pathway, that is usually impaired in obese humans, were also upregulated. Finally, genes related to antigen-processing and presentation were downregulated in the HIGH group. CONCLUSION Our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to to elucidate the effects of lipid deposition on muscle metabolism in pigs.
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Affiliation(s)
- Angela Cánovas
- IRTA, Genètica i Millora Animal, 191 Av Alcalde Rovira Roure, 25198 Lleida, Spain
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Profiling of histone H3 lysine 9 trimethylation levels predicts transcription factor activity and survival in acute myeloid leukemia. Blood 2010; 116:3564-71. [PMID: 20498303 DOI: 10.1182/blood-2009-09-240978] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Acute myeloid leukemia (AML) is commonly associated with alterations in transcription factors because of altered expression or gene mutations. These changes might induce leukemia-specific patterns of histone modifications. We used chromatin-immunoprecipitation on microarray to analyze histone 3 lysine 9 trimethylation (H3K9me3) patterns in primary AML (n = 108), acute lymphoid leukemia (n = 28), CD34(+) cells (n = 21) and white blood cells (n = 15) specimens. Hundreds of promoter regions in AML showed significant alterations in H3K9me3 levels. H3K9me3 deregulation in AML occurred preferentially as a decrease in H3K9me3 levels at core promoter regions. The altered genomic regions showed an overrepresentation of cis-binding sites for ETS and cyclic adenosine monophosphate response elements (CREs) for transcription factors of the CREB/CREM/ATF1 family. The decrease in H3K9me3 levels at CREs was associated with increased CRE-driven promoter activity in AML blasts in vivo. AML-specific H3K9me3 patterns were not associated with known cytogenetic abnormalities. But a signature derived from H3K9me3 patterns predicted event-free survival in AML patients. When the H3K9me3 signature was combined with established clinical prognostic markers, it outperformed prognosis prediction based on clinical parameters alone. These findings demonstrate widespread changes of H3K9me3 levels at gene promoters in AML. Signatures of histone modification patterns are associated with patient prognosis in AML.
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Kok M, Zwart W, Holm C, Fles R, Hauptmann M, Van't Veer LJ, Wessels LFA, Neefjes J, Stål O, Linn SC, Landberg G, Michalides R. PKA-induced phosphorylation of ERα at serine 305 and high PAK1 levels is associated with sensitivity to tamoxifen in ER-positive breast cancer. Breast Cancer Res Treat 2010; 125:1-12. [PMID: 20213082 DOI: 10.1007/s10549-010-0798-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 02/09/2010] [Indexed: 01/30/2023]
Abstract
Phosphorylation of estrogen receptor α at serine 305 (ERαS305-P) by protein kinase A (PKA) or p21-activated kinase 1 (PAK1) has experimentally been associated with tamoxifen sensitivity. Here, we investigated the clinical application of this knowledge to predict tamoxifen resistance in ER-positive breast cancer patients. Using immunohistochemistry, a score including PAK1 and co-expression of PKA and ERαS305-P (PKA/ERαS305-P) was developed on a training set consisting of 103 patients treated with tamoxifen for metastatic disease, and validated on 231 patients randomized between adjuvant tamoxifen or no treatment. In the training set, PAK1 levels were associated with tumor progression after tamoxifen (HR 1.57, 95% CI 0.99-2.48), as was co-expression of PKA and ERαS305-P (HR 2.00, 95% CI 1.14-3.52). In the validation set, a significant tamoxifen benefit was found among the 73% patients negative for PAK1 and PKA/ERαS305-P (HR 0.54, 95% CI 0.34-0.87), while others (27%) were likely to have no benefit from tamoxifen (HR 0.88, 95% 0.42-1.82). The test for interaction showed a significant difference in recurrence-free survival between groups defined by PAK1 and PKA/ERαS305-P (P = 0.037). Elevated PAK1 and PKA/ERαS305-P appeared to influence tamoxifen sensitivity. Both PAK1 and PKA/ERαS305-P levels were associated with sensitivity to tamoxifen in breast tumors and the combination of these variables should be considered in predicting tamoxifen benefit.
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Affiliation(s)
- Marleen Kok
- Department of Experimental Therapy, Netherlands Cancer Institute, Amsterdam, The Netherlands
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Abstract
DNA microarrays are powerful tools for studying biological mechanisms and for developing prognostic and predictive classifiers for identifying the patients who require treatment and are best candidates for specific treatments. Because microarrays produce so much data from each specimen, they offer great opportunities for discovery and great dangers or producing misleading claims. Microarray based studies require clear objectives for selecting cases and appropriate analysis methods. Effective analysis of microarray data, where the number of measured variables is orders of magnitude greater than the number of cases, requires specialized statistical methods which have recently been developed. Recent literature reviews indicate that serious problems of analysis exist a substantial proportion of publications. This manuscript attempts to provide a non-technical summary of the key principles of statistical design and analysis for studies that utilize microarray expression profiling.
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Affiliation(s)
- Richard Simon
- Biometric Research Branch, Division of Cancer Treatment & Diagnosis, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434, USA.
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Monaco A, Marincola FM, Sabatino M, Pos Z, Tornesello ML, Stroncek DF, Wang E, Lewis GK, Buonaguro FM, Buonaguro L. Molecular immune signatures of HIV-1 vaccines in human PBMCs. FEBS Lett 2009; 583:3004-8. [PMID: 19665024 PMCID: PMC3418664 DOI: 10.1016/j.febslet.2009.07.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 11/20/2022]
Abstract
The global transcriptional profile of peripheral blood mononuclear cells (PBMCs) stimulated with HIV candidate vaccine (virus-like particles, VLPs) has been evaluated in HIV-infected patients with low/high viral load compared to healthy volunteers. Baseline activation of chemokine production was observed in PBMC from HIV-infected patients and innate immune stimulation with HIV-VLPs was not blunted. The immune profile among HIV-infected patients was found to be qualitatively similar but quantitatively extremely variable. This diversity was independent of viral load and it might be dependent on individual immunogenetic traits or concurrent immunological status. This ex vivo screening strategy represents an efficient tool for guiding modifications/optimizations of vaccination strategies and understanding failures in individuals enrolled in clinical trials.
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Affiliation(s)
- Alessandro Monaco
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health Bethesda, MD, USA
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Nater UM, Whistler T, Lonergan W, Mletzko T, Vernon SD, Heim C. Impact of acute psychosocial stress on peripheral blood gene expression pathways in healthy men. Biol Psychol 2009; 82:125-32. [PMID: 19577611 PMCID: PMC7116965 DOI: 10.1016/j.biopsycho.2009.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 05/27/2009] [Accepted: 06/29/2009] [Indexed: 11/30/2022]
Abstract
We investigated peripheral blood mononuclear cell gene expression responses to acute psychosocial stress to identify molecular pathways relevant to the stress response. Blood samples were obtained from 10 healthy male subjects before, during and after (at 0, 30, and 60 min) a standardized psychosocial laboratory stressor. Ribonucleic acid (RNA) was extracted and gene expression measured by hybridization to a 20,000-gene microarray. Gene Set Expression Comparisons (GSEC) using defined pathways were used for the analysis. Forty-nine pathways were significantly changed from baseline to immediately after the stressor (p < 0.05), implicating cell cycle, cell signaling, adhesion and immune responses. The comparison between stress and recovery (measured 30 min later) identified 36 pathways, several involving stress-responsive signaling cascades and cellular defense mechanisms. These results have relevance for understanding molecular mechanisms of the physiological stress response, and might be used to further study adverse health outcomes of psychosocial stress.
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Affiliation(s)
- Urs M Nater
- Chronic Viral Diseases Branch, National Center for Zoonotic, Vector-borne and Enteric Diseases, Centers for Disease Control & Prevention, 1600 Clifton Rd, MS-G41, Atlanta, GA 30329, USA
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Nesnow S, Ward W, Moore T, Ren H, Hester SD. Discrimination of Tumorigenic Triazole Conazoles from Phenobarbital by Transcriptional Analyses of Mouse Liver Gene Expression. Toxicol Sci 2009; 110:68-83. [DOI: 10.1093/toxsci/kfp076] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Visne I, Dilaveroglu E, Vierlinger K, Lauss M, Yildiz A, Weinhaeusel A, Noehammer C, Leisch F, Kriegner A. RGG: a general GUI Framework for R scripts. BMC Bioinformatics 2009; 10:74. [PMID: 19254356 PMCID: PMC2653488 DOI: 10.1186/1471-2105-10-74] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 03/02/2009] [Indexed: 11/17/2022] Open
Abstract
Background R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. Results We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) – tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. Conclusion RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at
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Affiliation(s)
- Ilhami Visne
- Austrian Research Centers GmbH, ARC, Molecular Diagnostics, Seibersdorf, Austria.
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André F, Michiels S, Dessen P, Scott V, Suciu V, Uzan C, Lazar V, Lacroix L, Vassal G, Spielmann M, Vielh P, Delaloge S. Exonic expression profiling of breast cancer and benign lesions: a retrospective analysis. Lancet Oncol 2009; 10:381-90. [PMID: 19249242 DOI: 10.1016/s1470-2045(09)70024-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Gene-expression arrays have generated molecular predictors of relapse and drug sensitivity in breast cancer. We aimed to identify exons differently expressed in malignant and benign breast lesions and to generate a molecular classifier for breast-cancer diagnosis. METHODS 165 breast samples were obtained by fine-needle aspiration. Complementary DNA was hybridised on splice array. A nearest centroid prediction rule was developed to classify lesions as malignant or benign on a training set, and its performance was assessed on an independent validation set. A two-way ANOVA model identified probe sets with differential expression in malignant and benign lesions while adjusting for scan dates. FINDINGS 120 breast cancers and 45 benign lesions were included in the study. A molecular classifier for breast-cancer diagnosis with 1228 probe sets was generated from the training set (n=94). This signature accurately classified all samples (100% accuracy, 95% CI 96-100%). In the validation set (n=71), the molecular predictor accurately classified 68 of 71 tumours (96%, 88-99%). When the 165 samples were taken into account, 37 858 exon probe sets (5.4%) and 3733 genes (7.0%) were differently expressed in malignant and benign lesions (threshold: adjusted p<0.05). Genes involved in spliceosome assembly were significantly overexpressed in malignant disease (permutation p=0.002). In the same population of 165 samples, 956 exon probe sets presented both higher intensity and higher splice index in breast cancer than in benign lesions, although located on unchanged genes. INTERPRETATION Many exons are differently expressed by breast cancer and benign lesions, and alternative transcripts contribute to the molecular characteristics of breast malignancy. Development of molecular classifiers for breast-cancer diagnosis with fine-needle aspiration should be possible.
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Affiliation(s)
- Fabrice André
- Breast Cancer Unit, Department of Medical Oncology, Institut Gustave Roussy France, Villejuif, France
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Creighton CJ, Nagaraja AK, Hanash SM, Matzuk MM, Gunaratne PH. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions. RNA (NEW YORK, N.Y.) 2008; 14:2290-2296. [PMID: 18812437 PMCID: PMC2578856 DOI: 10.1261/rna.1188208] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/26/2008] [Indexed: 05/26/2023]
Abstract
MicroRNAs are short (approximately 22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches. However, integration of microRNA-mRNA target predictions with gene expression data on a large scale using these databases is currently cumbersome and time consuming for many researchers. We have developed a desktop software application which, for a given target prediction database, retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Furthermore, for each microRNA, the software computes an enrichment statistic for overrepresentation of predicted targets within the gene set, which could help to implicate roles for specific microRNAs and microRNA-regulated genes in the system under study. Currently, the software supports searching of results from PicTar, TargetScan, and miRanda algorithms. In addition, the software can accept any user-defined set of gene-to-class associations for searching, which can include the results of other target prediction algorithms, as well as gene annotation or gene-to-pathway associations. A search (using our software) of genes transcriptionally regulated in vitro by estrogen in breast cancer uncovered numerous targeting associations for specific microRNAs-above what could be observed in randomly generated gene lists-suggesting a role for microRNAs in mediating the estrogen response. The software and Excel VBA source code are freely available at http://sigterms.sourceforge.net.
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Affiliation(s)
- Chad J Creighton
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.
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Abstract
Using a question and answer format we describe important aspects of using genomic technologies in cancer research. The main challenges are not managing the mass of data, but rather the design, analysis, and accurate reporting of studies that result in increased biological knowledge and medical utility. Many analysis issues address the use of expression microarrays but are also applicable to other whole genome assays. Microarray-based clinical investigations have generated both unrealistic hype and excessive skepticism. Genomic technologies are tremendously powerful and will play instrumental roles in elucidating the mechanisms of oncogenesis and in bringing on an era of predictive medicine in which treatments are tailored to individual tumors. Achieving these goals involves challenges in rethinking many paradigms for the conduct of basic and clinical cancer research and for the organization of interdisciplinary collaboration.
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Affiliation(s)
- Richard Simon
- Biometric Research Branch, National Cancer Institute, Bethesda, MD 20892-7434, USA.
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Fang W, Li X, Jiang Q, Liu Z, Yang H, Wang S, Xie S, Liu Q, Liu T, Huang J, Xie W, Li Z, Zhao Y, Wang E, Marincola FM, Yao K. Transcriptional patterns, biomarkers and pathways characterizing nasopharyngeal carcinoma of Southern China. J Transl Med 2008; 6:32. [PMID: 18570662 PMCID: PMC2443113 DOI: 10.1186/1479-5876-6-32] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 06/20/2008] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The pathogenesis of nasopharyngeal carcinoma (NPC) is a complicated process involving genetic predisposition, Epstein-Bar Virus infection, and genetic alterations. Although some oncogenes and tumor suppressor genes have been previously reported in NPC, a complete understanding of the pathogenesis of NPC in the context of global gene expression, transcriptional pathways and biomarker assessment remains to be elucidated. METHODS Total RNA from 32 pathologically-confirmed cases of poorly-differentiated NPC was divided into pools inclusive of four consecutive specimens and each pool (T1 to T8) was co-hybridized with pooled RNA from 24 normal non-cancerous nasopharyngeal tissues (NP) to a human 8K cDNA array platform. The reliability of microarray data was validated for selected genes by semi-quantitative RT-PCR and immunohistochemistry. RESULTS Stringent statistical filtering parameters identified 435 genes to be up-regulated and 257 genes to be down-regulated in NPC compared to NP. Seven up-regulated genes including CYC1, MIF, LAMB3, TUBB2, UBE2C and TRAP1 had been previously proposed as candidate common cancer biomarkers based on a previous extensive comparison among various cancers and normal tissues which did not, however, include NPC or NP. In addition, nine known oncogenes and tumor suppressor genes, MIF, BIRC5, PTTG1, ATM, FOXO1A, TGFBR2, PRKAR1A, KLF5 and PDCD4 were identified through the microarray literature-based annotation search engine MILANO, suggesting these genes may be specifically involved in the promotion of the malignant conversion of nasopharyngeal epithelium. Finally, we found that these differentially expressed genes were involved in apoptosis, MAPK, VEGF and B cell receptor signaling pathways and other functions associated with cell growth, signal transduction and immune system activation. CONCLUSION This study identified potential candidate biomarkers, oncogenes/tumor suppressor genes involved in several pathways relevant to the oncogenesis of NPC. This information may facilitate the determination of diagnostic and therapeutic targets for NPC as well as provide insights about the molecular pathogenesis of NPC.
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Affiliation(s)
- Weiyi Fang
- Cancer Research Institute of Southern Medical University, Key Lab for Transcriptomics and Proteomics of Human Fatal Diseases Supported by Ministry of Education and Guangdong Province, 510515, PR China.
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Chalmel F, Primig M. The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. BMC Bioinformatics 2008; 9:86. [PMID: 18254954 PMCID: PMC2375118 DOI: 10.1186/1471-2105-9-86] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 02/06/2008] [Indexed: 11/10/2022] Open
Abstract
Background High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. Results We developed the Annotation, Mapping, Expression and Network (AMEN) software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i) uploading and pre-processing data from microarray expression profiling experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. Conclusion AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.
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Affiliation(s)
- Frédéric Chalmel
- Institut National de la Santé et de la Recherche Médicale Unité 625, Groupe d'Etude de la Reproduction chez l'Homme et les Mammifères, Institut Fédératif de Recherche 140, F-35042 Rennes, France.
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