1
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Joosten SE, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Collier MD, Morova T, Altintas B, Kim Y, Canisius S, Korkmaz G, Lack N, Vermeulen M, Linn SC, Zwart W. Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output. bioRxiv 2023:2023.10.30.564691. [PMID: 37961147 PMCID: PMC10634999 DOI: 10.1101/2023.10.30.564691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Estrogen Receptor alpha (ERα) is the main driver and prime drug target in luminal breast. ERα chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ERα chromatin action, along with its biological implications. Here, we use a large set of ERα ChIP-seq data from 70 ERα+ breast cancers to explore inter-patient heterogeneity in ERα DNA binding, to reveal a striking inter-tumor heterogeneity of ERα action. Interestingly, commonly-shared ERα sites showed the highest estrogen-driven enhancer activity and were most-engaged in long-range chromatin interactions. In addition, the most-commonly shared ERα-occupied enhancers were enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ERα and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we could confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ERα-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ERα landscape, with the most-common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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2
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Özkan H, Öztürk DG, Korkmaz G. Transcriptional Factor Repertoire of Breast Cancer in 3D Cell Culture Models. Cancers (Basel) 2022; 14:cancers14041023. [PMID: 35205770 PMCID: PMC8870600 DOI: 10.3390/cancers14041023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Knowledge of the transcriptional regulation of breast cancer tumorigenesis is largely based on studies performed in two-dimensional (2D) monolayer culture models, which lack tissue architecture and therefore fail to represent tumor heterogeneity. However, three-dimensional (3D) cell culture models are better at mimicking in vivo tumor microenvironment, which is critical in regulating cellular behavior. Hence, 3D cell culture models hold great promise for translational breast cancer research. Abstract Intratumor heterogeneity of breast cancer is driven by extrinsic factors from the tumor microenvironment (TME) as well as tumor cell–intrinsic parameters including genetic, epigenetic, and transcriptomic traits. The extracellular matrix (ECM), a major structural component of the TME, impacts every stage of tumorigenesis by providing necessary biochemical and biomechanical cues that are major regulators of cell shape/architecture, stiffness, cell proliferation, survival, invasion, and migration. Moreover, ECM and tissue architecture have a profound impact on chromatin structure, thereby altering gene expression. Considering the significant contribution of ECM to cellular behavior, a large body of work underlined that traditional two-dimensional (2D) cultures depriving cell–cell and cell–ECM interactions as well as spatial cellular distribution and organization of solid tumors fail to recapitulate in vivo properties of tumor cells residing in the complex TME. Thus, three-dimensional (3D) culture models are increasingly employed in cancer research, as these culture systems better mimic the physiological microenvironment and shape the cellular responses according to the microenvironmental cues that will regulate critical cell functions such as cell shape/architecture, survival, proliferation, differentiation, and drug response as well as gene expression. Therefore, 3D cell culture models that better resemble the patient transcriptome are critical in defining physiologically relevant transcriptional changes. This review will present the transcriptional factor (TF) repertoire of breast cancer in 3D culture models in the context of mammary tissue architecture, epithelial-to-mesenchymal transition and metastasis, cell death mechanisms, cancer therapy resistance and differential drug response, and stemness and will discuss the impact of culture dimensionality on breast cancer research.
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Affiliation(s)
- Hande Özkan
- School of Medicine, Koç University, Istanbul 34450, Turkey;
- Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Deniz Gülfem Öztürk
- School of Medicine, Koç University, Istanbul 34450, Turkey;
- Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
- Correspondence: (D.G.Ö.); (G.K.)
| | - Gozde Korkmaz
- School of Medicine, Koç University, Istanbul 34450, Turkey;
- Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
- Correspondence: (D.G.Ö.); (G.K.)
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3
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Li L, Ugalde AP, Scheele CLGJ, Dieter SM, Nagel R, Ma J, Pataskar A, Korkmaz G, Elkon R, Chien MP, You L, Su PR, Bleijerveld OB, Altelaar M, Momchev L, Manber Z, Han R, van Breugel PC, Lopes R, ten Dijke P, van Rheenen J, Agami R. A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis. Genome Biol 2021; 22:54. [PMID: 33514403 PMCID: PMC7845134 DOI: 10.1186/s13059-021-02272-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiveness. Although thousands of YAP/TEAD4 binding-sites are annotated, their functional importance is unknown. Here, we aim at further identification of enhancer elements that are required for YAP functions. RESULTS We first apply genome-wide ChIP profiling of YAP to systematically identify enhancers that are bound by YAP/TEAD4. Next, we implement a genetic approach to uncover functions of YAP/TEAD4-associated enhancers, demonstrate its robustness, and use it to reveal a network of enhancers required for YAP-mediated proliferation. We focus on EnhancerTRAM2, as its target gene TRAM2 shows the strongest expression-correlation with YAP activity in nearly all tumor types. Interestingly, TRAM2 phenocopies the YAP-induced cell proliferation, migration, and invasion phenotypes and correlates with poor patient survival. Mechanistically, we identify FSTL-1 as a major direct client of TRAM2 that is involved in these phenotypes. Thus, TRAM2 is a key novel mediator of YAP-induced oncogenic proliferation and cellular invasiveness. CONCLUSIONS YAP is a transcription co-factor that binds to thousands of enhancer loci and stimulates tumor aggressiveness. Using unbiased functional approaches, we dissect YAP enhancer network and characterize TRAM2 as a novel mediator of cellular proliferation, migration, and invasion. Our findings elucidate how YAP induces cancer aggressiveness and may assist diagnosis of cancer metastasis.
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Affiliation(s)
- Li Li
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Alejandro P. Ugalde
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Colinda L. G. J. Scheele
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Sebastian M. Dieter
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Remco Nagel
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Jin Ma
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
| | - Abhijeet Pataskar
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Gozde Korkmaz
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Miao-Ping Chien
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Li You
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pin-Rui Su
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Onno B. Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvt Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Lyubomir Momchev
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Zohar Manber
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ruiqi Han
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Pieter C. van Breugel
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Rui Lopes
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Peter ten Dijke
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
| | - Jacco van Rheenen
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
- Erasmus MC, Rotterdam University, Rotterdam, The Netherlands
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4
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Korkmaz G, Manber Z, Lopes R, Prekovic S, Schuurman K, Kim Y, Teunissen H, Flach K, Wit ED, Galli GG, Zwart W, Elkon R, Agami R. A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation. Nucleic Acids Res 2019; 47:9557-9572. [PMID: 31372638 PMCID: PMC6765117 DOI: 10.1093/nar/gkz675] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/11/2019] [Accepted: 07/24/2019] [Indexed: 01/07/2023] Open
Abstract
Estrogen receptor α (ERα) is an enhancer activating transcription factor, a key driver of breast cancer and a main target for cancer therapy. ERα-mediated gene regulation requires proper chromatin-conformation to facilitate interactions between ERα-bound enhancers and their target promoters. A major determinant of chromatin structure is the CCCTC-binding factor (CTCF), that dimerizes and together with cohesin stabilizes chromatin loops and forms the boundaries of topologically associated domains. However, whether CTCF-binding elements (CBEs) are essential for ERα-driven cell proliferation is unknown. To address this question in a global manner, we implemented a CRISPR-based functional genetic screen targeting CBEs located in the vicinity of ERα-bound enhancers. We identified four functional CBEs and demonstrated the role of one of them in inducing chromatin conformation changes in favor of activation of PREX1, a key ERα target gene in breast cancer. Indeed, high PREX1 expression is a bona-fide marker of ERα-dependency in cell lines, and is associated with good outcome after anti-hormonal treatment. Altogether, our data show that distinct CTCF-mediated chromatin structures are required for ERα- driven breast cancer cell proliferation.
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Affiliation(s)
- Gozde Korkmaz
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Zohar Manber
- Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rui Lopes
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Yongsoo Kim
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Koen Flach
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Giorgio G Galli
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands
| | - Ran Elkon
- Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Erasmus MC, Rotterdam University, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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5
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Li L, van Breugel PC, Loayza-Puch F, Ugalde AP, Korkmaz G, Messika-Gold N, Han R, Lopes R, Barbera EP, Teunissen H, de Wit E, Soares RJ, Nielsen BS, Holmstrøm K, Martínez-Herrera DJ, Huarte M, Louloupi A, Drost J, Elkon R, Agami R. LncRNA-OIS1 regulates DPP4 activation to modulate senescence induced by RAS. Nucleic Acids Res 2019; 46:4213-4227. [PMID: 29481642 PMCID: PMC5934637 DOI: 10.1093/nar/gky087] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/29/2018] [Indexed: 12/15/2022] Open
Abstract
Oncogene-induced senescence (OIS), provoked in response to oncogenic activation, is considered an important tumor suppressor mechanism. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nt without a protein-coding capacity. Functional studies showed that deregulated lncRNA expression promote tumorigenesis and metastasis and that lncRNAs may exhibit tumor-suppressive and oncogenic function. Here, we first identified lncRNAs that were differentially expressed between senescent and non-senescent human fibroblast cells. Using RNA interference, we performed a loss-function screen targeting the differentially expressed lncRNAs, and identified lncRNA-OIS1 (lncRNA#32, AC008063.3 or ENSG00000233397) as a lncRNA required for OIS. Knockdown of lncRNA-OIS1 triggered bypass of senescence, higher proliferation rate, lower abundance of the cell-cycle inhibitor CDKN1A and high expression of cell-cycle-associated genes. Subcellular inspection of lncRNA-OIS1 indicated nuclear and cytosolic localization in both normal culture conditions as well as following oncogene induction. Interestingly, silencing lncRNA-OIS1 diminished the senescent-associated induction of a nearby gene (Dipeptidyl Peptidase 4, DPP4) with established role in tumor suppression. Intriguingly, similar to lncRNA-OIS1, silencing DPP4 caused senescence bypass, and ectopic expression of DPP4 in lncRNA-OIS1 knockdown cells restored the senescent phenotype. Thus, our data indicate that lncRNA-OIS1 links oncogenic induction and senescence with the activation of the tumor suppressor DPP4.
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Affiliation(s)
- Li Li
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Pieter C van Breugel
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Fabricio Loayza-Puch
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Alejandro Pineiro Ugalde
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Gozde Korkmaz
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Naama Messika-Gold
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, 69978, Tel Aviv University, Tel Aviv, Israel
| | - Ruiqi Han
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Rui Lopes
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Eric P Barbera
- Division of Molecular Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | | | | | - Kim Holmstrøm
- Bioneer A/S, Kogle Allé 2, DK-2970 Hørsholm, Denmark
| | | | - Maite Huarte
- Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Annita Louloupi
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Jarno Drost
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, 69978, Tel Aviv University, Tel Aviv, Israel
| | - Reuven Agami
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.,Erasmus MC, Rotterdam University, 3000 CA Rotterdam, The Netherlands.,Oncode institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
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6
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Olmez-Hanci T, Arslan-Alaton I, Doğan M, Khoei S, Fakhri H, Korkmaz G. Enhanced degradation of micropollutants by zero-valent aluminum activated persulfate: assessment of toxicity and genotoxic activity. Water Sci Technol 2017; 76:3195-3204. [PMID: 29235998 DOI: 10.2166/wst.2017.489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Advanced oxidation of the aqueous Triton™ X-45 (TX-45), iopamidol (IOPA), ciprofloxacin (CIP) and bisphenol A (BPA) solutions via activation of persulfate (PS) with zero-valent aluminum (ZVA) was investigated. The study aimed at assessing the effectiveness of the PS/ZVA process in terms of target micropollutants (MPs) and toxicity abatements in raw surface water (RSW) and distilled water (DW). TX-45, CIP and BPA were completely degraded after 90-minute, 120-minute and 40-minute treatment, respectively, with PS/ZVA in DW, whereas 95% IOPA removal was achieved after 120-minute (MPs = 2 mg/L; ZVA = 1 g/L; PS = 0.25 mM for CIP and BPA; PS = 0.50 mM for TX-45 and IOPA; pH = 3). TX-45 (59%), IOPA (29%), CIP (73%) and BPA (46%) removal efficiencies decreased after 120-minute PS/ZVA treatment in RSW. In DW, Vibrio fischeri toxicities of original (untreated) MPs were found as: CIP (51%) > BPA (40%) > TX-45 (15%) > IOPA (1%), and as BPA (100%) > CIP (66%) > IOPA (62%) > TX-45 (35%) in RSW. Acute toxicities of MPs and their degradation products fluctuated during PS/ZVA treatment both in DW and RSW samples and resulted in different relative inhibition values after 120-minute. The original and PS/ZVA-treated TX-45, IOPA and BPA in DW exhibited neither cytotoxic nor genotoxic effects, whereas CIP oxidation ended up in degradation products with genotoxic effects.
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Affiliation(s)
- T Olmez-Hanci
- School of Civil Engineering, Department of Environmental Engineering, Istanbul Technical University, 34469 Maslak Istanbul, Turkey E-mail:
| | - I Arslan-Alaton
- School of Civil Engineering, Department of Environmental Engineering, Istanbul Technical University, 34469 Maslak Istanbul, Turkey E-mail:
| | - M Doğan
- School of Civil Engineering, Department of Environmental Engineering, Istanbul Technical University, 34469 Maslak Istanbul, Turkey E-mail:
| | - S Khoei
- School of Civil Engineering, Department of Environmental Engineering, Istanbul Technical University, 34469 Maslak Istanbul, Turkey E-mail:
| | - H Fakhri
- School of Civil Engineering, Department of Environmental Engineering, Istanbul Technical University, 34469 Maslak Istanbul, Turkey E-mail:
| | - G Korkmaz
- School of Civil Engineering, Department of Environmental Engineering, Istanbul Technical University, 34469 Maslak Istanbul, Turkey E-mail:
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7
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Abstract
The advent of next-generation sequencing (NGS) technologies has revolutionized the way we do research on gene expression. High-throughput transcriptomics became possible with the development of microarray technology, but its widespread application only occurred after the emergence of massive parallel sequencing. Especially, RNA sequencing (RNA-seq) has greatly increased our knowledge about the genome and led to the identification and annotation of novel classes of RNAs in different species. However, RNA-seq measures the steady-state level of a given RNA, which is the equilibrium between transcription, processing, and degradation. In recent years, a number of dedicated RNA-seq technologies were developed to measure specifically transcription events. Global run-on sequencing (GRO-seq) is the most widely used method to measure nascent RNA, and in recent years, it has been applied successfully to study the function and mechanism of action of noncoding RNAs. Here, we describe a detailed protocol of GRO-seq that can be readily applied to investigate different aspects of RNA biology in human cells.
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Affiliation(s)
- Rui Lopes
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.
- Erasmus MC, Rotterdam University, Rotterdam, The Netherlands.
| | - Gozde Korkmaz
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.
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8
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Abstract
The development of the CRISPR-Cas9 system triggered a revolution in the field of genome engineering. Initially, the use of this system was focused on the study of protein-coding genes but, recently, a number of CRISPR-Cas9-based tools have been developed to study non-coding transcriptional regulatory elements. These technological advances offer unprecedented opportunities for elucidating the functions of enhancers in their endogenous context. Here, we discuss the application, current limitations and future development of CRISPR-Cas9 systems to identify and characterize enhancer elements in a high-throughput manner.
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Affiliation(s)
- Rui Lopes
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Gozde Korkmaz
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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9
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Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, Zwart W, Elkon R, Agami R. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat Biotechnol 2016; 34:192-8. [PMID: 26751173 DOI: 10.1038/nbt.3450] [Citation(s) in RCA: 289] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/08/2015] [Indexed: 01/03/2023]
Abstract
Systematic identification of noncoding regulatory elements has, to date, mainly relied on large-scale reporter assays that do not reproduce endogenous conditions. We present two distinct CRISPR-Cas9 genetic screens to identify and characterize functional enhancers in their native context. Our strategy is to target Cas9 to transcription factor binding sites in enhancer regions. We identified several functional enhancer elements and characterized the role of two of them in mediating p53 (TP53) and ERα (ESR1) gene regulation. Moreover, we show that a genomic CRISPR-Cas9 tiling screen can precisely map functional domains within enhancer elements. Our approach expands the utility of CRISPR-Cas9 to elucidate the functions of the noncoding genome.
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Affiliation(s)
- Gozde Korkmaz
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rui Lopes
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Alejandro P Ugalde
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ekaterina Nevedomskaya
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ruiqi Han
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ksenia Myacheva
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Wilbert Zwart
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ran Elkon
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands.,Erasmus MC, Rotterdam University, Rotterdam, the Netherlands
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10
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Elkon R, Loayza-Puch F, Korkmaz G, Lopes R, van Breugel PC, Bleijerveld OB, Altelaar AFM, Wolf E, Lorenzin F, Eilers M, Agami R. Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. EMBO Rep 2015; 16:1723-36. [PMID: 26538417 PMCID: PMC4687422 DOI: 10.15252/embr.201540717] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/21/2015] [Indexed: 12/15/2022] Open
Abstract
c‐Myc is one of the major human proto‐oncogenes and is often associated with tumor aggression and poor clinical outcome. Paradoxically, Myc was also reported as a suppressor of cell motility, invasiveness, and metastasis. Among the direct targets of Myc are many components of the protein synthesis machinery whose induction results in an overall increase in protein synthesis that empowers tumor cell growth. At present, it is largely unknown whether beyond the global enhancement of protein synthesis, Myc activation results in translation modulation of specific genes. Here, we measured Myc‐induced global changes in gene expression at the transcription, translation, and protein levels and uncovered extensive transcript‐specific regulation of protein translation. Particularly, we detected a broad coordination between regulation of transcription and translation upon modulation of Myc activity and showed the connection of these responses to mTOR signaling to enhance oncogenic transformation and to the TGFβ pathway to modulate cell migration and invasiveness. Our results elucidate novel facets of Myc‐induced cellular responses and provide a more comprehensive view of the consequences of its activation in cancer cells.
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Affiliation(s)
- Ran Elkon
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fabricio Loayza-Puch
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gozde Korkmaz
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rui Lopes
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pieter C van Breugel
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Onno B Bleijerveld
- Mass Spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - A F Maarten Altelaar
- Mass Spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Centre Cancer Genomics Centre, Utrecht, The Netherlands
| | - Elmar Wolf
- Biozentrum der Universität Würzburg Theodor Boveri Institut Am Hubland, Würzburg, Germany
| | - Francesca Lorenzin
- Biozentrum der Universität Würzburg Theodor Boveri Institut Am Hubland, Würzburg, Germany
| | - Martin Eilers
- Biozentrum der Universität Würzburg Theodor Boveri Institut Am Hubland, Würzburg, Germany
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands Erasmus MC, Rotterdam University, Rotterdam, The Netherlands
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11
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Korkmaz G, Inal B, Ortakoylu G, Irmak H, Kara A, Gelisgen R, Ogurlu O, Uzun H. Changes in Oxidative Stress Parameters and Antioxidant Status in Lung Cancer: Western Blot Analysis of Nitrotyrosine and Protein Carbonyls Content. Clin Lab 2014; 60:599-607. [DOI: 10.7754/clin.lab.2013.130407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Korkmaz G, Tekirdag KA, Ozturk DG, Kosar A, Sezerman OU, Gozuacik D. MIR376A is a regulator of starvation-induced autophagy. PLoS One 2013; 8:e82556. [PMID: 24358205 PMCID: PMC3864973 DOI: 10.1371/journal.pone.0082556] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/29/2013] [Indexed: 01/07/2023] Open
Abstract
Background Autophagy is a vesicular trafficking process responsible for the degradation of long-lived, misfolded or abnormal proteins, as well as damaged or surplus organelles. Abnormalities of the autophagic activity may result in the accumulation of protein aggregates, organelle dysfunction, and autophagy disorders were associated with various diseases. Hence, mechanisms of autophagy regulation are under exploration. Methods Over-expression of hsa-miR-376a1 (shortly MIR376A) was performed to evaluate its effects on autophagy. Autophagy-related targets of the miRNA were predicted using Microcosm Targets and MIRanda bioinformatics tools and experimentally validated. Endogenous miRNA was blocked using antagomirs and the effects on target expression and autophagy were analyzed. Luciferase tests were performed to confirm that 3′ UTR sequences in target genes were functional. Differential expression of MIR376A and the related MIR376B was compared using TaqMan quantitative PCR. Results Here, we demonstrated that, a microRNA (miRNA) from the DLK1/GTL2 gene cluster, MIR376A, played an important role in autophagy regulation. We showed that, amino acid and serum starvation-induced autophagy was blocked by MIR376A overexpression in MCF-7 and Huh7 cells. MIR376A shared the same seed sequence and had overlapping targets with MIR376B, and similarly blocked the expression of key autophagy proteins ATG4C and BECN1 (Beclin 1). Indeed, 3′ UTR sequences in the mRNA of these autophagy proteins were responsive to MIR376A in luciferase assays. Antagomir tests showed that, endogenous MIR376A was participating to the control of ATG4C and BECN1 transcript and protein levels. Moreover, blockage of endogenous MIR376A accelerated starvation-induced autophagic activity. Interestingly, MIR376A and MIR376B levels were increased with different kinetics in response to starvation stress and tissue-specific level differences were also observed, pointing out to an overlapping but miRNA-specific biological role. Conclusions Our findings underline the importance of miRNAs encoded by the DLK1/GTL2 gene cluster in stress-response control mechanisms, and introduce MIR376A as a new regulator of autophagy.
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Affiliation(s)
- Gozde Korkmaz
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Kumsal Ayse Tekirdag
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Deniz Gulfem Ozturk
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Ali Kosar
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Osman Ugur Sezerman
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Devrim Gozuacik
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- * E-mail:
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13
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Tekirdag KA, Korkmaz G, Ozturk DG, Agami R, Gozuacik D. MIR181A regulates starvation- and rapamycin-induced autophagy through targeting of ATG5. Autophagy 2013; 9:374-85. [PMID: 23322078 DOI: 10.4161/auto.23117] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macroautophagy (autophagy herein) is a cellular catabolic mechanism activated in response to stress conditions including starvation, hypoxia and misfolded protein accumulation. Abnormalities in autophagy were associated with pathologies including cancer and neurodegenerative diseases. Hence, elucidation of the signaling pathways controlling autophagy is of utmost importance. Recently we and others described microRNAs (miRNAs) as novel and potent modulators of the autophagic activity. Here, we describe MIR181A (hsa-miR-181a-1) as a new autophagy-regulating miRNA. We showed that overexpression of MIR181A resulted in the attenuation of starvation- and rapamycin-induced autophagy in MCF-7, Huh-7 and K562 cells. Moreover, antagomir-mediated inactivation of endogenous miRNA activity stimulated autophagy. We identified ATG5 as an MIR181A target. Indeed, ATG5 cellular levels were decreased in cells upon MIR181A overexpression and increased following the introduction of antagomirs. More importantly, overexpression of ATG5 from a miRNA-insensitive cDNA construct rescued autophagic activity in the presence of MIR181A. We also showed that the ATG5 3' UTR contained functional MIR181A responsive sequences sensitive to point mutations. Therefore, MIR181A is a novel and important regulator of autophagy and ATG5 is a rate-limiting miRNA target in this effect.
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Affiliation(s)
- Kumsal Ayse Tekirdag
- Faculty of Engineering and Natural Sciences, Biological Sciences and Bioengineering Program, Sabanci University, Istanbul, Turkey
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14
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Kuzuoglu-Ozturk D, Cebeci Yalcinkaya O, Akpinar BA, Mitou G, Korkmaz G, Gozuacik D, Budak H. Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response. Planta 2012; 236:1081-92. [PMID: 22569921 DOI: 10.1007/s00425-012-1657-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 04/16/2012] [Indexed: 05/02/2023]
Abstract
An autophagy-related gene Atg8 was cloned for the first time from wild emmer wheat, named as TdAtg8, and its role on autophagy under abiotic stress conditions was investigated. Examination of TdAtg8 expression patterns indicated that Atg8 expression was strongly upregulated under drought stress, especially in the roots when compared to leaves. LysoTracker(®) red marker, utilized to observe autophagosomes, revealed that autophagy is constitutively active in Triticum dicoccoides. Moreover, autophagy was determined to be induced in plants exposed to osmotic stress when compared to plants grown under normal conditions. Functional studies were executed in yeast to confirm that the TdATG8 protein is functional, and showed that the TdAtg8 gene complements the atg8∆::kan MX yeast mutant strain grown under nitrogen deficiency. For further functional analysis, TdATG8 protein was expressed in yeast and analyzed using Western immunoblotting. Atg8-silenced plants were exposed to drought stress and chlorophyll and malondialdehyde (MDA) content measurements demonstrated that Atg8 plays a key role on drought stress tolerance. In addition, Atg8-silenced plants exposed to osmotic stress were found to have decreased Atg8 expression level in comparison to controls. Hence, Atg8 is a positive regulator in osmotic and drought stress response.
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Affiliation(s)
- Duygu Kuzuoglu-Ozturk
- Biological Sciences and Bioengineering Program, Sabanci University, Tuzla, Istanbul, Turkey
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15
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Korkmaz G, le Sage C, Tekirdag KA, Agami R, Gozuacik D. miR-376b controls starvation and mTOR inhibition-related autophagy by targeting ATG4C and BECN1. Autophagy 2012; 8:165-76. [PMID: 22248718 DOI: 10.4161/auto.8.2.18351] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Macroautophagy (autophagy) is the major intracellular degradation pathway for long-lived proteins and organelles. It helps the cell to survive a spectrum of stressful conditions including starvation, growth factor deprivation and misfolded protein accumulation. Moreover, abnormalities of autophagy play a role in major health problems including cancer and neurodegenerative diseases. Yet, mechanisms controlling autophagic activity are not fully understood. Here, we describe hsa-miR-376b (miR-376b) as a new microRNA (miRNA) regulating autophagy. We showed that miR-376b expression attenuated starvation- and rapamycin-induced autophagy in MCF-7 and Huh-7 cells. We discovered autophagy proteins ATG4C and BECN1 (Beclin 1) as cellular targets of miR-376b. Indeed, upon miRNA overexpression, both mRNA and protein levels of ATG4C and BECN1 were decreased. miR-376b target sequences were present in the 3' UTR of ATG4C and BECN1 mRNAs and introduction of mutations abolished their miR-376b responsiveness. Antagomir-mediated inactivation of the endogenous miR-376b led to an increase in ATG4C and BECN1 levels. Therefore, miR-376b controls autophagy by directly regulating intracellular levels of two key autophagy proteins, ATG4C and BECN1.
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Affiliation(s)
- Gozde Korkmaz
- Faculty of Engineering and Natural Sciences, Biological Sciences and Bioengineering Program, Sabanci University, Orhanli-Tuzla, Istanbul, Turkey
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Abstract
We report 6 new cases of congenital esophageal stenosis (CES) that presented to us with special diagnostic and management problems and review the literature on this subject. Gastroesophageal reflux and achalasia are important differential diagnoses of esophageal stenosis, they may be associated with CES making appropriate management even more difficult. Treatment is also controversial, ranging from simple dilatation to segmental resection. CES should be present in every pediatric surgeon's mind should dysphagia occur on the introduction of semisolid food or esophageal food impaction, with a segmental stenosis demonstrated at esophagogram even when more obvious diagnoses are evoked.
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Affiliation(s)
- N Diab
- Hotel Dieu de France, Department of Pediatric Surgery, Beirut, Lebanon
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Abstract
We report our series of 16 children with 23 megaureters: 7 were refluxing, 11 were obstructive (7 primary and 4 secondary), 3 both refluxing and obstructive and 2 nonrefluxing nonobstructive. These patients had a Kalicinski folding-under remodeling of their megaureter and Cohen or Lead-better reimplantation. Success rate was 96% with only 2 failures: 1 recurrent low-grade reflux treated with subureteric Teflon injection and 1 stenosis that necessitated reoperation. Kalicinski's technique with Cohen type reimplantation is one of the best alternatives for megaureters, mainly because it does not present the disadvantages of the excisional procedure.
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Affiliation(s)
- P Daher
- Department of Pediatrics, Hôtel-Dieu de France Hospital, Université Saint Joseph, Faculté de Médecine, Beirut, Libanon
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18
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Haddad-Zebouni S, Daher P, Ghoraib Z, Nammour F, Slaba S, Korkmaz G, Atallah N. [Role of ultrasonography in the diagnosis of acute appendicitis in children. Apropos of 35 cases]. J Med Liban 1998; 46:79-83. [PMID: 10095832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Abstract
We hereby report the third case of antenatal diagnosis of congenital cyst of the pancreas. It is a very rare lesion and could present as a differential diagnosis of any intra-abdominal cystic mass. Early treatment is easy and prevents complications such as ascites and pancreatitis in case of intra-pancreatic enteric duplication.
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Affiliation(s)
- P Daher
- Département de Chirurgie Pédiatrique et de Pédiatrie, Hospital Hôtel Dieu de France, CHU de l'Université St Joseph, Beyrouth, Liban
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Abstract
We report the fifth case of congenital prepubic sinus that goes from the anterior wall of the bladder through the public symphysis to the skin. The various embryological theories that could be responsible for this pathology are discussed, and according to us, it seems to be a variant of dorsal urethral duplication.
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Affiliation(s)
- P Daher
- Department of Pediatric Surgery, Hôtel-Dieu de France, Beirut, Lebanon
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Ziylan YZ, Korkmaz G, Bernard G, Lefauconnier JM. Effect of dimethyl sulfoxide on blood-to-brain transfer of alpha-aminoisobutyric acid: examination of regional blood-brain barrier function. Neurosci Lett 1988; 89:74-9. [PMID: 2456498 DOI: 10.1016/0304-3940(88)90483-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The effect of dimethyl sulfoxide (DMSO) on brain capillary permeability has been controversial. We have studied the effect of DMSO on unidirectional transport of alpha-aminoisobutyric acid (AIB) across the blood-brain barrier (BBB) in rats. Rats were treated with 15% DMSO intraperitoneally (i.p.), intravenously (i.v.) or by an i.p. injection in combination with an i.v. injection, or in some cases intra-arterially by rapid infusion into left external carotid artery. The unidirectional blood-to-brain transfer constant (Ki) for AIB was measured in each group after the animals were killed. DMSO administration did not significantly increase Ki as compared to control Kj. These results show that it is unlikely that DMSO increases the permeability of BBB and therefore do not support the proposal that DMSO can act as a carrier at the BBB for compounds with restricted vascular permeability.
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Affiliation(s)
- Y Z Ziylan
- Department of Physiology, Istanbul Faculty of Medicine, Turkey
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22
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Korkmaz G, David M, Parchoux B, Souillet G, Lauras B, Chavrier Y, Campo-Paysaa A. [Aseptic osteonecrosis following corticoid therapy and immunodepressive agents in children. Apropos of 3 observations]. Pediatrie 1975; 30:463-76. [PMID: 1178273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Floret D, Korkmaz G, David M, Bertrand J, Jeune M. [Hip-joint lesions and their course in congenital myxedema in children. Apropos of 59 cases]. Pediatrie 1974; 29:495-525. [PMID: 4431698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Campo-Paysaa A, Jeaubert de Beaujeu M, Chavrier Y, Korkmaz G, Daudet M, Chappuis JP. [183 cases of Hirschsprung's disease. Analysis of therapeutic results]. Pediatrie 1973; 28:649-55. [PMID: 4787374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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25
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Jaubert de Beaujeu M, Chavrier Y, Campo-Paysaa A, Ezra P, Korkmaz G. [An unusual complication of closed thoracic injuries: intercostal pulmonary hernia]. Lyon Chir 1971; 67:225-7. [PMID: 5567207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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Chappuis JP, Daudet M, Lerat JL, Fournier P, Korkmaz G. [Microbial spondylodiskitis in the vertebral pathology of the child. 15 cases]. Ann Chir Infant 1969; 10:475-94. [PMID: 5365765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Fischer L, Imbert JC, David M, Comtet JJ, Korkmaz G, Chavatte JP. [Traumatic luxation successively affecting both hips in a child: predisposing factors]. Lyon Med 1969; 222:263-6 passim. [PMID: 5398816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Marion J, Daudet M, Chappuis JP, Korkmaz G. [Osteomyelitic arthritis of the hip in young infants: alarming reminder of its frequency and its functional severity (52 cases)]. Pediatrie 1969; 24:655-67. [PMID: 5402794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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29
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Rebouillat J, Truchet P, Korkmaz G. [Lengthening of the tibia in treatment of inequalities of leg lengths]. Lyon Chir 1968; 64:786-94. [PMID: 5745974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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