1
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Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci. Nat Genet 2021; 53:650-662. [PMID: 33972799 DOI: 10.1038/s41588-021-00842-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 03/10/2021] [Indexed: 12/18/2022]
Abstract
In cancer cells, enhancer hijacking mediated by chromosomal alterations and/or increased deposition of acetylated histone H3 lysine 27 (H3K27ac) can support oncogene expression. However, how the chromatin conformation of enhancer-promoter interactions is affected by these events is unclear. In the present study, by comparing chromatin structure and H3K27ac levels in normal and lymphoma B cells, we show that enhancer-promoter-interacting regions assume different conformations according to the local abundance of H3K27ac. Genetic or pharmacological depletion of H3K27ac decreases the frequency and the spreading of these interactions, altering oncogene expression. Moreover, enhancer hijacking mediated by chromosomal translocations influences the epigenetic status of the regions flanking the breakpoint, prompting the formation of distinct intrachromosomal interactions in the two homologous chromosomes. These interactions are accompanied by allele-specific gene expression changes. Overall, our work indicates that H3K27ac dynamics modulates interaction frequency between regulatory regions and can lead to allele-specific chromatin configurations to sustain oncogene expression.
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2
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Asadi M, Ganjibakhsh M, Aghdam SM, Izadpanah M, Moghanjoghi SM, Gorji ZE, Rahmati H, Amoli AD, Movassagh SA, Fazeli SAS, Farhangniya M, Farzaneh P. Establishment and Preservation of Lymphoblastoid Cell Lines from Fresh and Frozen Whole Blood and Mononuclear Cells. In Vitro Cell Dev Biol Anim 2020; 56:332-340. [PMID: 32358742 DOI: 10.1007/s11626-020-00431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/08/2020] [Indexed: 10/24/2022]
Abstract
Although blood cells are interesting sources for genome investigations, one of the main problems in obtaining genomic DNA from blood is the restricted amount of DNA. This obstacle can be avoided by generating Epstein-Barr virus (EBV)-induced B cell lines. This study investigates the efficiency of four different methods to generate lymphoblastoid cell lines (LCLs). Blood samples (n = 120) were obtained from donors and categorized into four groups: fresh whole blood, frozen whole blood, fresh peripheral blood mononuclear cells (PBMCs), and frozen PBMCs. The samples were followed by EBV transformation to generate LCLs. Quality control and authentication of the cells were performed using multiplex PCR and short tandem repeat (STR) analyses. Finally, we assessed the success rate and amount of time to establish the cell lines in each group. The results showed that the cells were not contaminated nor were they misidentified or cross-contaminated with other cells. The success rate of LCLs generated from the whole blood groups was lower than the PBMC groups. The freezing procedures did not have any considerable effect on the establishment of lymphoblastoid cells. These established cells have been preserved in the human and animal cell bank of the Iranian Biological Resource Center (IBRC) and are available for researchers. Due to the management and transformation of a substantial number of blood samples, we recommend that researchers freeze PBMCs for further use with high efficiency and time-saving. We suggest that whole fresh blood should be directly transformed when the volume of the blood sample is less than 0.5 ml.
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Affiliation(s)
- Masoumeh Asadi
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Meysam Ganjibakhsh
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Samaneh Mahmoud Aghdam
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Mehrnaz Izadpanah
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Shiva Mohamadi Moghanjoghi
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran.,Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Elyasi Gorji
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Hedieh Rahmati
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | | | | | - Seyed Abolhassan Shahzadeh Fazeli
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran.,Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Mansoureh Farhangniya
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Parvaneh Farzaneh
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran.
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3
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Hu SY, Zhuang QQ, Qiu Y, Zhu XF, Yan QF. Cell models and drug discovery for mitochondrial diseases. J Zhejiang Univ Sci B 2019; 20:449-456. [PMID: 31090270 DOI: 10.1631/jzus.b1900196] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Mitochondrion is a semi-autonomous organelle, important for cell energy metabolism, apoptosis, the production of reactive oxygen species (ROS), and Ca2+ homeostasis. Mitochondrial DNA (mtDNA) mutation is one of the primary factors in mitochondrial disorders. Though much progress has been made, there remain many difficulties in constructing cell models for mitochondrial diseases. This seriously restricts studies related to targeted drug discovery and the mechanism and therapy for such diseases. Here we summarize the characteristics of patient-specific immortalized lymphoblastoid cells, fibroblastoid cells, cytoplasmic hybrid (cybrid) cell lines, and induced pluripotent stem cells (iPSCs)-derived differentiation cells in the study of mitochondrial disorders, as well as offering discussion of roles and advances of these cell models, particularly in the screening of drugs.
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Affiliation(s)
- Shuang-Yi Hu
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qian-Qian Zhuang
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yue Qiu
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xu-Fen Zhu
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qing-Feng Yan
- Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.,Department of Pediatrics, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou 310058, China
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4
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Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. Sci Data 2019; 6:112. [PMID: 31273215 PMCID: PMC6609777 DOI: 10.1038/s41597-019-0116-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/07/2019] [Indexed: 01/23/2023] Open
Abstract
In biomedical research, lymphoblastoid cell lines (LCLs), often established by in vitro infection of resting B cells with Epstein-Barr virus, are commonly used as surrogates for peripheral blood lymphocytes. Genomic and transcriptomic information on LCLs has been used to study the impact of genetic variation on gene expression in humans. Here we present single-cell RNA sequencing (scRNA-seq) data on GM12878 and GM18502—two LCLs derived from the blood of female donors of European and African ancestry, respectively. Cells from three samples (the two LCLs and a 1:1 mixture of the two) were prepared separately using a 10x Genomics Chromium Controller and deeply sequenced. The final dataset contained 7,045 cells from GM12878, 5,189 from GM18502, and 5,820 from the mixture, offering valuable information on single-cell gene expression in highly homogenous cell populations. This dataset is a suitable reference for population differentiation in gene expression at the single-cell level. Data from the mixture provide additional valuable information facilitating the development of statistical methods for data normalization and batch effect correction. Design Type(s) | transcription profiling design • strain comparison design | Measurement Type(s) | transcription profiling assay | Technology Type(s) | RNA sequencing | Factor Type(s) | ancestry status • sex | Sample Characteristic(s) | GM12878 cell • GM18502 cell • immortal human peripheral vein-derived B cell line cell |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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5
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Matejka K, Stückler F, Salomon M, Ensenauer R, Reischl E, Hoerburger L, Grallert H, Kastenmüller G, Peters A, Daniel H, Krumsiek J, Theis FJ, Hauner H, Laumen H. Dynamic modelling of an ACADS genotype in fatty acid oxidation - Application of cellular models for the analysis of common genetic variants. PLoS One 2019; 14:e0216110. [PMID: 31120904 PMCID: PMC6532850 DOI: 10.1371/journal.pone.0216110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/15/2019] [Indexed: 11/19/2022] Open
Abstract
Background Genome-wide association studies of common diseases or metabolite quantitative traits often identify common variants of small effect size, which may contribute to phenotypes by modulation of gene expression. Thus, there is growing demand for cellular models enabling to assess the impact of gene regulatory variants with moderate effects on gene expression. Mitochondrial fatty acid oxidation is an important energy metabolism pathway. Common noncoding acyl-CoA dehydrogenase short chain (ACADS) gene variants are associated with plasma C4-acylcarnitine levels and allele-specific modulation of ACADS expression may contribute to the observed phenotype. Methods and findings We assessed ACADS expression and intracellular acylcarnitine levels in human lymphoblastoid cell lines (LCL) genotyped for a common ACADS variant associated with plasma C4-acylcarnitine and found a significant genotype-dependent decrease of ACADS mRNA and protein. Next, we modelled gradual decrease of ACADS expression using a tetracycline-regulated shRNA-knockdown of ACADS in Huh7 hepatocytes, a cell line with high fatty acid oxidation-(FAO)-capacity. Assessing acylcarnitine flux in both models, we found increased C4-acylcarnitine levels with decreased ACADS expression levels. Moreover, assessing time-dependent changes of acylcarnitine levels in shRNA-hepatocytes with altered ACADS expression levels revealed an unexpected effect on long- and medium-chain fatty acid intermediates. Conclusions Both, genotyped LCL and regulated shRNA-knockdown are valuable tools to model moderate, gradual gene-regulatory effects of common variants on cellular phenotypes. Decreasing ACADS expression levels modulate short and surprisingly also long/medium chain acylcarnitines, and may contribute to increased plasma acylcarnitine levels.
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Affiliation(s)
- Kerstin Matejka
- Chair of Nutritional Medicine, Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- ZIEL-Research Center for Nutrition and Food Sciences, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, Neuherberg, Germany
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Technische Universität München, Freising-Weihenstephan, Germany
| | - Ferdinand Stückler
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Regina Ensenauer
- Research Center, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Universität München, München, Germany
- Experimental Pediatrics and Metabolism, Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children’s Hospital, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Child Nutrition, Max Rubner-Institut, Karlsruhe, Germany
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lena Hoerburger
- Paediatric Nutritional Medicine, Else Kröner-Fresenius-Centre for Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, Neuherberg, Germany
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Technische Universität München, Freising-Weihenstephan, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK-Munich partner site), Neuherberg, Germany
| | - Hannelore Daniel
- ZIEL-Research Center for Nutrition and Food Sciences, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- Chair of Physiology of Human Nutrition, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Jan Krumsiek
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States of America
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Mathematical Science, Technische Universität München, Garching, Germany
- * E-mail: (FJT); (HL)
| | - Hans Hauner
- Chair of Nutritional Medicine, Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- ZIEL-Research Center for Nutrition and Food Sciences, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, Neuherberg, Germany
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Technische Universität München, Freising-Weihenstephan, Germany
- Else Kröner-Fresenius-Center for Nutritional Medicine, Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Helmut Laumen
- Chair of Nutritional Medicine, Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- ZIEL-Research Center for Nutrition and Food Sciences, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, Neuherberg, Germany
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Technische Universität München, Freising-Weihenstephan, Germany
- Paediatric Nutritional Medicine, Else Kröner-Fresenius-Centre for Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Research Unit Protein Science, Helmholtz Zentrum München, Neuherberg, Germany
- * E-mail: (FJT); (HL)
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6
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Biospecimen Science of Blood for Peripheral Blood Mononuclear Cell (PBMC) Functional Applications. CURRENT PATHOBIOLOGY REPORTS 2019. [DOI: 10.1007/s40139-019-00192-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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A modified protocol for highly efficient EBV-mediated immortalization of human B lymphocytes from small volumes of peripheral blood serum. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2018. [DOI: 10.1016/j.ejmhg.2017.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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8
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Legut M, Dolton G, Mian AA, Ottmann OG, Sewell AK. CRISPR-mediated TCR replacement generates superior anticancer transgenic T cells. Blood 2018; 131:311-322. [PMID: 29122757 PMCID: PMC5774207 DOI: 10.1182/blood-2017-05-787598] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/04/2017] [Indexed: 12/20/2022] Open
Abstract
Adoptive transfer of T cells genetically modified to express a cancer-specific T-cell receptor (TCR) has shown significant therapeutic potential for both hematological and solid tumors. However, a major issue of transducing T cells with a transgenic TCR is the preexisting expression of TCRs in the recipient cells. These endogenous TCRs compete with the transgenic TCR for surface expression and allow mixed dimer formation. Mixed dimers, formed by mispairing between the endogenous and transgenic TCRs, may harbor autoreactive specificities. To circumvent these problems, we designed a system where the endogenous TCR-β is knocked out from the recipient cells using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9) technology, simultaneously with transduction with a cancer-reactive receptor of choice. This TCR replacement strategy resulted in markedly increased surface expression of transgenic αβ and γδ TCRs, which in turn translated to a stronger, and more polyfunctional, response of engineered T cells to their target cancer cell lines. Additionally, the TCR-plus-CRISPR-modified T cells were up to a thousandfold more sensitive to antigen than standard TCR-transduced T cells or conventional model proxy systems used for studying TCR activity. Finally, transduction with a pan-cancer-reactive γδ TCR used in conjunction with CRISPR/Cas9 knockout of the endogenous αβ TCR resulted in more efficient redirection of CD4+ and CD8+ T cells against a panel of established blood cancers and primary, patient-derived B-cell acute lymphoblastic leukemia blasts compared with standard TCR transfer. Our results suggest that TCR transfer combined with genome editing could lead to new, improved generations of cancer immunotherapies.
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Affiliation(s)
- Mateusz Legut
- Division of Infection and Immunity, School of Medicine
- Systems Immunity Research Institute, and
| | - Garry Dolton
- Division of Infection and Immunity, School of Medicine
- Systems Immunity Research Institute, and
| | - Afsar Ali Mian
- Haematology, Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Oliver G Ottmann
- Haematology, Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine
- Systems Immunity Research Institute, and
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9
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Tousizadeh B, Moghim S, Chaleshtori ARS, Ghanbarian M, Mirian M, Salehi M, Tousizadeh S, Zaboli F. Application of Epstein-Barr Virus for Optimization of Immortalized B-lymphocyte Production as a Positive Control in Genetic Studies. Adv Biomed Res 2017; 6:80. [PMID: 28808646 PMCID: PMC5539668 DOI: 10.4103/2277-9175.210659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Infection of B-cells with Epstein-Barr virus (EBV) leads to more and subsequent immortalization. This is considered as the method of choice for generating lymphoblastoid cell lines (LCLs). Producing LCLs, although very useful but is very time consuming and troublesome, drives the requirement for quicker and more reliable methods for EBV-driven B-cell transformation. MATERIALS AND METHODS After successfully production of LCLs, different parameters including temperature, serum concentration, type of culture medium, and CO2 concentration were evaluated on EBV-transformed B-cells. In this study, we were able to produce LCLs and optimize condition. RESULTS The best condition for generating LCLs was 37°C, 5% CO2, 20% fasting blood sugar, and RPMI 1640. The study results were to establish a reliable method for producing LCLs that can be used to produce immortalized B-cells from almost any sources. CONCLUSION This can help with tumorgenecity studies, as well as producing control material for rare genetic disorders and so on. The aim of this study was to determine optimized condition for reliable and reproducible LCLs from different sources.
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Affiliation(s)
- Behnaz Tousizadeh
- Department of Microbiology, Faculty of Basic Sciences, Ayatollah Amoli Azad University, Amol, Iran.,Pediatric Inherited Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Maryam Ghanbarian
- Department of Microbiology, Faculty of Basic Science, Islamic Azad University, Falavarjan Branch, Isfahan, Iran
| | - Mina Mirian
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Department of Microbiology, Faculty of Basic Sciences, Ayatollah Amoli Azad University, Amol, Iran.,Medical Genetics Center of Genome, Isfahan, Iran.,Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sepideh Tousizadeh
- Department of Health, School of Health, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Fatemeh Zaboli
- Department of Microbiology, Faculty of Basic Sciences, Ayatollah Amoli Azad University, Amol, Iran
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10
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Liu X, Xu C, Duan Z. A Simple Red Blood Cell Lysis Method for the Establishment of B Lymphoblastoid Cell Lines. J Vis Exp 2017. [PMID: 28117797 DOI: 10.3791/55191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A number of methods exist for the transformation of B lymphocytes by the Epstein Barr virus in vitro into immortalized cell lines. We have developed a new method with a powerful and simple strategy for the establishment of B-LCLs, the red blood cell lysis method. This method simplified the PBMC separation procedure with red blood cell removal, and used as little as 0.5 mL of whole blood for establishing EBV-immortalized cell lines, which can proliferate to large cell numbers in a relatively short amount time with a 100% success rate. The method is simple, reliable, time saving, and applicable to treating a large number of the clinical samples.
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Affiliation(s)
- Xi Liu
- Wuhan Institute of Virology, Chinese Academy of Sciences; Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
| | - Chongfeng Xu
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
| | - Ziyuan Duan
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences;
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11
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Abdel Malak CA, Abelhafez TH, Tabll AA, Mashaly MM, El Shenawy R, El-Abd YS, Shaker MH, El-Awady MK. Neutralizing activity and safety of human monoclonal antibodies against hepatitis C virus. Hum Antibodies 2017; 26:127-134. [PMID: 29036810 DOI: 10.3233/hab-170330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AIM Assessment of the neutralizing activity of human monoclonal antibodies against HCV and also study their safety in experimental small animals (Swiss mice). MATERIALS AND METHODS Assessment of neutralizing activity of human monoclonal antibodies against HCV envelope regions (E1, E2) by two methods: by HCV cc infectious system 1) and by using positive HCV positive serum as source of HCV particles genotype 4a (neutralizing assay 2). Dot ELISA was used to study the activity of the generated antibodies. Safety and toxicity of the generated human antibodies were tested by assessing the changes in the biochemistry of liver function and kidney function tests, Complete blood counts (CBC) and studying the pathological changes with different concentrations of purified human antibodies were carried out.. RESULTS Human Abs # 5 & 11 showed neutralizing activity by (neutralizing assay 2) but were not neutralizing by HCV cc assay. Human Abs # 12 & 15 showed neutralizing activity by the two methods i.e our generated human antibodies Abs# 5 &11 & 12 & 15 were neutralizing for HCV genotype 4a and Abs # 12 & 15 were neutralizing for HCV genotypes 4a and 2a. Liver and kidney functions and CBC results indicated that doses of 10 μg, 100 μg were safe. The histopathological results indicated that the dose of 10 μg of purified human monoclonal antibodies per mouse body weight was safe. CONCLUSION The generated human monoclonal antibodies can be used to develop potent immunotherapy agents that can be administrated for the post-transplantation patients to prevent the recurrence of HCV infection. Also, the monoclonal antibodies can be used to develop a candidate vaccine against HCV.
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Affiliation(s)
| | - Tawfeek H Abelhafez
- Department of Microbial Biotechnology, National Research Center, Giza, Egypt
| | - Ashraf A Tabll
- Department of Microbial Biotechnology, National Research Center, Giza, Egypt
| | - Mohammad M Mashaly
- Department of Chemistry, Faculty of Science, Damietta University, Damietta, Egypt
| | - Reem El Shenawy
- Department of Microbial Biotechnology, National Research Center, Giza, Egypt
| | - Yasmine S El-Abd
- Department of Microbial Biotechnology, National Research Center, Giza, Egypt
| | | | - Mostafa K El-Awady
- Department of Microbial Biotechnology, National Research Center, Giza, Egypt
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12
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Purwada A, Singh A. Immuno-engineered organoids for regulating the kinetics of B-cell development and antibody production. Nat Protoc 2016; 12:168-182. [PMID: 28005068 DOI: 10.1038/nprot.2016.157] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Induction of B-cell immunity against infection depends on the initiation of the germinal center (GC) reaction in secondary lymphoid organs. Ex vivo recapitulation of the GC reaction in 2D cultures results in transient cell growth, with poor yield and short-term survival. Furthermore, no reported 2D ex vivo system can modulate the kinetics of a GC-like phenotype or the rate of antibody class switching. This protocol describes a methodology for developing immune organoids that partially mimic the B-cell zone of a lymphoid tissue, for efficient and rapid generation of B cells with a GC-like phenotype from naive murine B cells. The organoid is composed of a bioadhesive protein, gelatin, that is transformed into an ionically cross-linked hydrated network using biocompatible silicate nanoparticles (SiNPs). We explain how to establish the immune organoid culture to sustain immune cell proliferation and transformation into a GC-like phenotype. Starting with cell encapsulation in digested lymphoid tissues, clusters of proliferating B cells with a GC-like phenotype can be generated in the organoids at controlled rates, within ∼1 week. The culture methodology described here is currently the only one that allows the accelerated induction of a GC-like phenotype in B cells and supports a controllable immunoglobulin class-switching reaction. This method can be easily implemented in a typical tissue culture room by personnel with standard mammalian cell culture expertise.
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Affiliation(s)
- Alberto Purwada
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Ankur Singh
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
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13
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Fujimori K, Tezuka T, Ishiura H, Mitsui J, Doi K, Yoshimura J, Tada H, Matsumoto T, Isoda M, Hashimoto R, Hattori N, Takahashi T, Morishita S, Tsuji S, Akamatsu W, Okano H. Modeling neurological diseases with induced pluripotent cells reprogrammed from immortalized lymphoblastoid cell lines. Mol Brain 2016; 9:88. [PMID: 27716287 PMCID: PMC5046991 DOI: 10.1186/s13041-016-0267-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022] Open
Abstract
Patient-specific induced pluripotent stem cells (iPSCs) facilitate understanding of the etiology of diseases, discovery of new drugs and development of novel therapeutic interventions. A frequently used starting source of cells for generating iPSCs has been dermal fibroblasts (DFs) isolated from skin biopsies. However, there are also numerous repositories containing lymphoblastoid B-cell lines (LCLs) generated from a variety of patients. To date, this rich bioresource of LCLs has been underused for generating iPSCs, and its use would greatly expand the range of targeted diseases that could be studied by using patient-specific iPSCs. However, it remains unclear whether patient’s LCL-derived iPSCs (LiPSCs) can function as a disease model. Therefore, we generated Parkinson’s disease patient-specific LiPSCs and evaluated their utility as tools for modeling neurological diseases. We established iPSCs from two LCL clones, which were derived from a healthy donor and a patient carrying PARK2 mutations, by using existing non-integrating episomal protocols. Whole genome sequencing (WGS) and comparative genomic hybridization (CGH) analyses showed that the appearance of somatic variations in the genomes of the iPSCs did not vary substantially according to the original cell types (LCLs, T-cells and fibroblasts). Furthermore, LiPSCs could be differentiated into functional neurons by using the direct neurosphere conversion method (dNS method), and they showed several Parkinson’s disease phenotypes that were similar to those of DF-iPSCs. These data indicate that the global LCL repositories can be used as a resource for generating iPSCs and disease models. Thus, LCLs are the powerful tools for generating iPSCs and modeling neurological diseases.
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Affiliation(s)
- Koki Fujimori
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Toshiki Tezuka
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan
| | - Hirobumi Tada
- Department of Physiology, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Kanagawa, 236-0027, Japan.,Department of Integrative Aging Neuroscience, Section of Neuroendocrinology, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Takuya Matsumoto
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan.,Institute for Innovation, Ajinomoto Co., Inc., Kawasaki-ku, Kanagawa, 210-8681, Japan
| | - Miho Isoda
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Ryota Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita-shi, Osaka, 565-0871, Japan.,Department of Psychiatry, Osaka University Graduate School of Medicine, Suita-shi, Osaka, 565-0871, Japan
| | - Nubutaka Hattori
- Department of Neurology, Juntendo University, School of Medicine, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Takuya Takahashi
- Department of Physiology, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Kanagawa, 236-0027, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan.,Medical Genome Center, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Medical Genome Center, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Wado Akamatsu
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan. .,Center for Genomic and Regenerative Medicine, Juntendo University, School of Medicine, Bunkyo-ku, Tokyo, 113-8431, Japan.
| | - Hideyuki Okano
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan.
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14
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Rzezniczek S, Obuchowicz M, Datka W, Siwek M, Dudek D, Kmiotek K, Oved K, Shomron N, Gurwitz D, Pilc A. Decreased sensitivity to paroxetine-induced inhibition of peripheral blood mononuclear cell growth in depressed and antidepressant treatment-resistant patients. Transl Psychiatry 2016; 6:e827. [PMID: 27244236 PMCID: PMC5545648 DOI: 10.1038/tp.2016.90] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 02/07/2016] [Accepted: 02/11/2016] [Indexed: 02/07/2023] Open
Abstract
Major depression disorder (MDD) is the most widespread mental disorder. Selective serotonin reuptake inhibitors (SSRIs) are used as first-line MDD treatment but are effective in <70% of patients. Thus, biomarkers for the early identification of treatment-resistant (TR) MDD patients are needed for prioritizing them for alternative therapeutics. SSRI-induced inhibition of the growth of peripheral blood mononuclear cells (PBMCs) is mediated via their target, the serotonin transporter (SERT). Here, we examined whether antidepressant drug-induced inhibition of the growth of PBMCs differed between MDD patients and healthy controls. PBMCs from well-characterized 33 treatment-sensitive (TS) and 33 TR MDD patients, and 24 healthy volunteers were studied. Dose-dependent inhibition of PBMCs growth was observed for both the non-SSRI antidepressant mirtazapine and the SSRI antidepressant paroxetine. Significantly lower sensitivities to 20 μm paroxetine were observed in MDD compared with control PBMCs prior to treatment onset (13% and 46%, respectively; P<0.05). Following antidepressant drug treatment for 4 or 7 weeks, the ex vivo paroxetine sensitivity increased to control levels in PBMCs from TS but not from TR MDD patients. This suggests that the low ex vivo paroxetine sensitivity phenotype reflects a state marker of depression. A significantly lower expression of integrin beta-3 (ITGB3), a co-factor of the SERT, was observed in the PBMCs of MDD patients prior to treatment onset compared with healthy controls, and may explain their lower paroxetine sensitivity. Further studies with larger cohorts are required for clarifying the potential of reduced PBMCs paroxetine sensitivity and lower ITGB3 expression as MDD biomarkers.
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Affiliation(s)
- S Rzezniczek
- Department of Neurobiology, Institute of Pharmacology Polish Academy of Science, Krakow, Poland,Department of Neurobiology, Institute of Pharmacology Polish Academy of Science, Smetna 12 Street, Krakow 31-343, Poland. E-mail:
| | - M Obuchowicz
- Department of Neurobiology, Institute of Pharmacology Polish Academy of Science, Krakow, Poland
| | - W Datka
- Department of Affective Disorders, Chair of Psychiatry, Jagiellonian University Medical College, Krakow, Poland
| | - M Siwek
- Department of Affective Disorders, Chair of Psychiatry, Jagiellonian University Medical College, Krakow, Poland
| | - D Dudek
- Department of Affective Disorders, Chair of Psychiatry, Jagiellonian University Medical College, Krakow, Poland
| | - K Kmiotek
- Department of Affective Disorders, Chair of Psychiatry, Jagiellonian University Medical College, Krakow, Poland
| | - K Oved
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Department of Cell and Developmental Biology, Tel Aviv University, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - N Shomron
- Department of Cell and Developmental Biology, Tel Aviv University, Sackler Faculty of Medicine, Tel Aviv, Israel,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - D Gurwitz
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - A Pilc
- Department of Neurobiology, Institute of Pharmacology Polish Academy of Science, Krakow, Poland,Institute of Public Health, Faculty of Health Sciences, Jagiellonian University, Krakow, Poland
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15
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Esanov R, Belle KC, van Blitterswijk M, Belzil VV, Rademakers R, Dickson DW, Petrucelli L, Boylan KB, Dykxhoorn DM, Wuu J, Benatar M, Wahlestedt C, Zeier Z. C9orf72 promoter hypermethylation is reduced while hydroxymethylation is acquired during reprogramming of ALS patient cells. Exp Neurol 2015; 277:171-177. [PMID: 26746986 DOI: 10.1016/j.expneurol.2015.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/17/2015] [Accepted: 12/29/2015] [Indexed: 12/13/2022]
Abstract
Among several genetic mutations known to cause amyotrophic lateral sclerosis (ALS), a hexanucleotide repeat expansion in the C9orf72 gene is the most common. In approximately 30% of C9orf72-ALS cases, 5-methylcytosine (5mC) levels within the C9orf72 promoter are increased, resulting in a modestly attenuated phenotype. The developmental timing of C9orf72 promoter hypermethylation and the reason why it occurs in only a subset of patients remain unknown. In order to model the acquisition of C9orf72 hypermethylation and examine the potential role of 5-hydroxymethylcytosine (5hmC), we generated induced pluripotent stem cells (iPSCs) from an ALS patient with C9orf72 promoter hypermethylation. Our data show that 5mC levels are reduced by reprogramming and then re-acquired upon neuronal specification, while 5hmC levels increase following reprogramming and are highest in iPSCs and motor neurons. We confirmed the presence of 5hmC within the C9orf72 promoter in post-mortem brain tissues of hypermethylated patients. These findings show that iPSCs are a valuable model system for examining epigenetic perturbations caused by the C9orf72 mutation and reveal a potential role for cytosine demethylation.
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Affiliation(s)
- Rustam Esanov
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kinsley C Belle
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, USA
| | | | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Kevin B Boylan
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, USA
| | - Joanne Wuu
- Department of Neurology, University of Miami Miller School of Medicine, USA
| | - Michael Benatar
- Department of Neurology, University of Miami Miller School of Medicine, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Zane Zeier
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA.
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16
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Niu N, Wang L. In vitro human cell line models to predict clinical response to anticancer drugs. Pharmacogenomics 2015; 16:273-85. [PMID: 25712190 DOI: 10.2217/pgs.14.170] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In vitro human cell line models have been widely used for cancer pharmacogenomic studies to predict clinical response, to help generate pharmacogenomic hypothesis for further testing, and to help identify novel mechanisms associated with variation in drug response. Among cell line model systems, immortalized cell lines such as Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) have been used most often to test the effect of germline genetic variation on drug efficacy and toxicity. Another model, especially in cancer research, uses cancer cell lines such as the NCI-60 panel. These models have been used mainly to determine the effect of somatic alterations on response to anticancer therapy. Even though these cell line model systems are very useful for initial screening, results from integrated analyses of multiple omics data and drug response phenotypes using cell line model systems still need to be confirmed by functional validation and mechanistic studies, as well as validation studies using clinical samples. Future models might include the use of patient-specific inducible pluripotent stem cells and the incorporation of 3D culture which could further optimize in vitro cell line models to improve their predictive validity.
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Affiliation(s)
- Nifang Niu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
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17
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Cheng S, Li J, Liu W, Liu C, Su L, Liu X, Guo L, Ma Y, Song B, Liu J. LTA + 252A > G polymorphism is associated with risk of nasal NK/T-cell lymphoma in a Chinese population: a case-control study. BMC Cancer 2015; 15:480. [PMID: 26108796 PMCID: PMC4490687 DOI: 10.1186/s12885-015-1506-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 06/19/2015] [Indexed: 11/25/2022] Open
Abstract
Background Nasal NK/T-cell lymphoma is a rare type of lymphoma in Caucasian individuals, but is relatively common in Asian populations. Genetic variants in immune and inflammatory response genes may thus be associated with the risk of developing lymphoma. Here, we investigated the association between immuno-modulatory gene polymorphisms and risk for nasal NK/T-cell lymphoma in a Chinese population. Methods Analysis of 12 single nucleotide polymorphisms (SNPs) in IL-10, TNF-α, lymphotoxin-α (LTA), and CTLA-4 genes was performed for 125 patients with NK/T-cell lymphoma and 300 healthy controls by PCR-ligase detection reactions. Results The LTA +252 GA + AA genotypes were associated with increased risk for NK/T-cell lymphoma (OR = 2.96, 95 % CI = 1.42–6.19, P = 0.004 for GA + AA genotype). Haplotype C-G-G-A (TNF-α -857, -308, −238 and LTA +252) also conferred an increased risk (OR = 1.52, 95 % CI = 1.14–2.06, P = 0.005). Additionally, the LTA +252 GA + AA genotype was associated with an even higher risk in populations positive for Epstein–Barr virus (OR = 5.20, 95 % CI = 1.22–23.41, P = 0.03 for the GA + AA genotype). Conclusions Our data suggest that the LTA +252 A > G polymorphism is associated with the risk of developing NK/T-cell lymphoma, especially for Epstein–Barr virus-positive NK/T-cell lymphoma in the Chinese population.
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Affiliation(s)
- Sensen Cheng
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China. .,School of Medicine and Life Sciences, University of Jinan, Shandong Academy of Medical Sciences, Jinan, China.
| | - Jianzhong Li
- Department of Oncology, General Hospital of Jinan Iron and Steel Group Limited Company, Jinan, China.
| | - Wenjian Liu
- Department of Oncology, Affiliated Hospital of Taishan Medical College, Taian, China.
| | - Chengxiang Liu
- Department of Oncology, General Hospital of Jinan Iron and Steel Group Limited Company, Jinan, China.
| | - Lei Su
- Department of Oncology, Zhangqiu People's Hospital of Shandong Province, Jinan, China.
| | - Xiuchun Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China.
| | - Liangjun Guo
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China.
| | - Yuan Ma
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China. .,School of Medicine and Life Sciences, University of Jinan, Shandong Academy of Medical Sciences, Jinan, China.
| | - Bao Song
- Basic Laboratory, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China.
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, China.
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Abstract
BACKGROUND Inflammatory bowel disease (IBD) is typically diagnosed at 20 to 40 years of age. However, very young versus elderly patients with IBD may have different mechanisms of disease that may affect prognosis and care. OBJECTIVES The purpose of this work was to identify single nucleotide polymorphisms associated with age of onset of Crohn's disease and ulcerative colitis. DESIGN Patients were genotyped using a custom microarray chip containing 332 IBD-associated single nucleotide polymorphisms. Age at diagnosis as a continuous variable was assessed using linear regression. Patients were then subgrouped by age at diagnosis and compared by the Fisher exact test. Bonferroni correction was used in all of the analyses. SETTINGS This study was conducted at a tertiary academic hospital. PATIENTS Sixty patients with Crohn's disease and 26 with ulcerative colitis were ≤ 16 years old, 259 patients with Crohn's disease and 248 with ulcerative colitis were 17-60 years old, and 10 patients with Crohn's disease and 20 with ulcerative colitis were >60 years old at diagnosis and included in this study. MAIN OUTCOME MEASURES Age at diagnosis and single nucleotide polymorphism correlations were measured in this study. RESULTS The NOD2 single nucleotide polymorphism rs2076756 was associated with younger age at Crohn's disease diagnosis (p = 0.0002). Patients with the AA/wild-type genotype were diagnosed at 31.9 ± 1.23 years, AG heterozygotes at 25.6 ± 0.99 years, and GG/at-risk allele homozygotes at 22.6 ± 1.32 years. Depending on age categories compared, single nucleotide polymorphisms in POU5F1, TNFSF15, and HLA DRB1*501 were associated with age of Crohn's disease diagnosis. No genetic associations were seen between ulcerative colitis and linear age at diagnosis; however, the G allele of the LAMB1 single nucleotide polymorphism rs886774 was found to be associated with ulcerative colitis diagnosed at ≤ 16 versus >17 years old (p = 0.008). LIMITATIONS This study was limited to known IBD single nucleotide polymorphisms. CONCLUSIONS This analysis reaffirms the association between NOD2, a molecule of innate immunity, and early Crohn's disease onset. This is the first report of a possible association between early Crohn's disease and the POU5F1, TNFSF15, and HLA DRB1*501 genes. The LAMB1 gene, associated with mucosal basement membrane integrity, was associated with early onset ulcerative colitis and, thus, suggests a fundamentally different mechanism of early disease pathogenesis in ulcerative colitis versus Crohn's disease.
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19
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Bernig T, Richter N, Volkmer I, Staege MS. Functional analysis and molecular characterization of spontaneously outgrown human lymphoblastoid cell lines. Mol Biol Rep 2014; 41:6995-7007. [PMID: 25037273 DOI: 10.1007/s11033-014-3587-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 07/05/2014] [Indexed: 01/14/2023]
Abstract
In vitro, the infection of human B-cells with the lymphotropic gammaherpesvirus Epstein-Barr virus (EBV) induces formation of permanently growing lymphoblastoid cell lines (LCL). In a spontaneously outgrown LCL (cell line CSIII), we detected nucleotide sequence variations of the EBV nuclear antigen 1 (EBNA1) RNA that was different from the reference sequence of EBNA1 in the prototypic EBV strain B95-8. In the present study, we molecularly and functionally characterized this virus isolate in comparison to LCL with the prototypic nucleotide sequence. Although we detected high functional similarity between CSIII and the other LCL, our data suggest that the lytic cycle might be ineffective in the CSIII LCL. DNA microarray analysis indicated that RNA binding motif, single stranded interacting protein 1 (RBMS1), which is typically expressed in latency III of EBV to prevent the lytic cycle, was the most overexpressed gene in CSIII LCL.
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Affiliation(s)
- Toralf Bernig
- Department of Pediatrics, Children's Cancer Research Centre, Martin Luther University Halle-Wittenberg, Ernst-Grube Str. 40, D-06097, Halle, Germany
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20
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Welch RP, Lee C, Imbriano PM, Patil S, Weymouth TE, Smith RA, Scott LJ, Sartor MA. ChIP-Enrich: gene set enrichment testing for ChIP-seq data. Nucleic Acids Res 2014; 42:e105. [PMID: 24878920 PMCID: PMC4117744 DOI: 10.1093/nar/gku463] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because it is often positively associated with the presence of one or more peaks and because many biologically defined gene sets have an excess of genes with longer or shorter gene locus lengths. Unlike alternative methods, ChIP-Enrich can account for the wide range of gene locus length-to-peak presence relationships (observed in ENCODE ChIP-seq data sets). We show that ChIP-Enrich has a well-calibrated type I error rate using permuted ENCODE ChIP-seq data sets; in contrast, two commonly used gene set enrichment methods, Fisher's exact test and the binomial test implemented in Genomic Regions Enrichment of Annotations Tool (GREAT), can have highly inflated type I error rates and biases in ranking. We identify DNA-binding proteins, including CTCF, JunD and glucocorticoid receptor α (GRα), that show different enrichment patterns for peaks closer to versus further from transcription start sites. We also identify known and potential new biological functions of GRα. ChIP-Enrich is available as a web interface (http://chip-enrich.med.umich.edu) and Bioconductor package.
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Affiliation(s)
- Ryan P Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chee Lee
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul M Imbriano
- Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA
| | - Snehal Patil
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Terry E Weymouth
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - R Alex Smith
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura J Scott
- Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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21
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Maurer M, Müller AC, Parapatics K, Pickl WF, Wagner C, Rudashevskaya EL, Breitwieser FP, Colinge J, Garg K, Griss J, Bennett KL, Wagner SN. Comprehensive comparative and semiquantitative proteome of a very low number of native and matched epstein-barr-virus-transformed B lymphocytes infiltrating human melanoma. J Proteome Res 2014; 13:2830-45. [PMID: 24803318 DOI: 10.1021/pr401270y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Melanoma, the deadliest form of skin cancer, is highly immunogenic and frequently infiltrated with immune cells including B cells. The role of tumor-infiltrating B cells (TIBCs) in melanoma is as yet unresolved, possibly due to technical challenges in obtaining TIBCs in sufficient quantity for extensive studies and due to the limited life span of B cells in vitro. A comprehensive workflow has thus been developed for successful isolation and proteomic analysis of a low number of TIBCs from fresh, human melanoma tissue. In addition, we generated in vitro-proliferating TIBC cultures using simultaneous stimulation with Epstein-Barr virus (EBV) and the TLR9 ligand CpG-oligodesoxynucleotide (CpG ODN). The FASP method and iTRAQ labeling were utilized to obtain a comparative, semiquantitative proteome to assess EBV-induced changes in TIBCs. By using as few as 100 000 B cells (∼5 μg protein)/sample for our proteomic study, a total number of 6507 proteins were identified. EBV-induced changes in TIBCs are similar to those already reported for peripheral B cells and largely involve changes in cell cycle proliferation, apoptosis, and interferon response, while most of the proteins were not significantly altered. This study provides an essential, further step toward detailed characterization of TIBCs including functional in vitro analysis.
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Affiliation(s)
- Margarita Maurer
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna , Waehringer Guertel 18-20, A-1090 Vienna, Austria
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22
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Connelly TM, Berg AS, Harris LR, Brinton DL, Hegarty JP, Deiling SM, Stewart DB, Koltun WA. Ulcerative colitis neoplasia is not associated with common inflammatory bowel disease single-nucleotide polymorphisms. Surgery 2014; 156:253-62. [PMID: 24947639 DOI: 10.1016/j.surg.2014.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 03/07/2014] [Indexed: 12/25/2022]
Abstract
BACKGROUND Neoplasia complicating ulcerative colitis (UC-neoplasia) is a problem that is poorly addressed by present surveillance techniques. The association of greater than 300 single nucleotide polymorphisms (SNPs) with inflammatory bowel disease (IBD) suggests the possibility that certain genetic polymorphisms might identify patients with UC destined for malignant degeneration. This present study tested the hypothesis that presently known IBD-associated SNPs may correlate with UC-neoplasia. MATERIALS AND METHODS A total of 41 patients with UC-neoplasia (mean age 56 ± 2.1 years) were identified from our divisional IBD Biobank (low-grade dysplasia n = 13, high-grade dysplasia n = 8, colorectal cancer [CRC] n = 20). These patients were individually age, sex, and disease duration matched with UC patients without neoplasia. Primary sclerosing cholangitis and family history of CRC were recorded. Patients were genotyped for 314 of the most commonly IBD-associated SNPs by a custom SNP microarray. Logistic regression and Fischer exact test were used for statistical analysis. RESULTS After Bonferroni correction, none of the 314 IBD-associated SNPs correlated with UC-neoplasia when compared with matched UC controls. The incidence of primary sclerosing cholangitis was greater in the UC-neoplasia group (10/41, 24% vs 3/41, 7%; P = .03) compared with UC controls. The severity of neoplasia (low grade dysplasia versus high grade dysplasia versus CRC) correlated with disease duration (7.9 vs 13.4 vs 20.7 years, respectively). CONCLUSION The lack of correlation between well-known IBD-associated SNPs and UC-neoplasia demonstrated in this study suggests that the development of neoplasia in patients with UC is associated with genetic determinants other than those that predispose to inflammation or results from posttranslational modifications or epigenetic factors rather than germline polymorphisms.
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Affiliation(s)
- Tara M Connelly
- Division of Colon and Rectal Surgery, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Arthur S Berg
- Department of Biostatistics, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Leonard R Harris
- Division of Colon and Rectal Surgery, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - David L Brinton
- Division of Colon and Rectal Surgery, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - John P Hegarty
- Division of Colon and Rectal Surgery, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Sue M Deiling
- Division of Colon and Rectal Surgery, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - David B Stewart
- Division of Colon and Rectal Surgery, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Walter A Koltun
- Division of Colon and Rectal Surgery, College of Medicine, The Pennsylvania State University, Hershey, PA.
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Ashraf S, Gee HY, Woerner S, Xie LX, Vega-Warner V, Lovric S, Fang H, Song X, Cattran DC, Avila-Casado C, Paterson AD, Nitschké P, Bole-Feysot C, Cochat P, Esteve-Rudd J, Haberberger B, Allen SJ, Zhou W, Airik R, Otto EA, Barua M, Al-Hamed MH, Kari JA, Evans J, Bierzynska A, Saleem MA, Böckenhauer D, Kleta R, El Desoky S, Hacihamdioglu DO, Gok F, Washburn J, Wiggins RC, Choi M, Lifton RP, Levy S, Han Z, Salviati L, Prokisch H, Williams DS, Pollak M, Clarke CF, Pei Y, Antignac C, Hildebrandt F. ADCK4 mutations promote steroid-resistant nephrotic syndrome through CoQ10 biosynthesis disruption. J Clin Invest 2013; 123:5179-89. [PMID: 24270420 DOI: 10.1172/jci69000] [Citation(s) in RCA: 237] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 09/06/2013] [Indexed: 12/14/2022] Open
Abstract
Identification of single-gene causes of steroid-resistant nephrotic syndrome (SRNS) has furthered the understanding of the pathogenesis of this disease. Here, using a combination of homozygosity mapping and whole human exome resequencing, we identified mutations in the aarF domain containing kinase 4 (ADCK4) gene in 15 individuals with SRNS from 8 unrelated families. ADCK4 was highly similar to ADCK3, which has been shown to participate in coenzyme Q10 (CoQ10) biosynthesis. Mutations in ADCK4 resulted in reduced CoQ10 levels and reduced mitochondrial respiratory enzyme activity in cells isolated from individuals with SRNS and transformed lymphoblasts. Knockdown of adck4 in zebrafish and Drosophila recapitulated nephrotic syndrome-associated phenotypes. Furthermore, ADCK4 was expressed in glomerular podocytes and partially localized to podocyte mitochondria and foot processes in rat kidneys and cultured human podocytes. In human podocytes, ADCK4 interacted with members of the CoQ10 biosynthesis pathway, including COQ6, which has been linked with SRNS and COQ7. Knockdown of ADCK4 in podocytes resulted in decreased migration, which was reversed by CoQ10 addition. Interestingly, a patient with SRNS with a homozygous ADCK4 frameshift mutation had partial remission following CoQ10 treatment. These data indicate that individuals with SRNS with mutations in ADCK4 or other genes that participate in CoQ10 biosynthesis may be treatable with CoQ10.
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A single nucleotide polymorphism in the STAT5 gene favors colonic as opposed to small-bowel inflammation in Crohn's disease. Dis Colon Rectum 2013; 56:1068-74. [PMID: 23929016 DOI: 10.1097/dcr.0b013e31829de128] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Crohn's disease is a chronic inflammatory ailment that can affect the colon and/or small intestine. A genetic basis for disease distribution is being sought, although the available data are seminal. The STAT5 gene is known to influence colonic permeability, mucosal regeneration, and interleukin 2 production, although its role in the distribution of Crohn's disease is unclear. OBJECTIVE The aim of this study was identification of single nucleotide polymorphisms associated with Crohn's distribution, with the goal of distinguishing disease subcategories and differing pathophysiologies. DESIGN This was a retrospective cohort study. SETTING The study was conducted in a single tertiary referral center. PATIENTS A total of 173 patients with Crohn's disease who were identified from our biobank were segregated by disease distribution (colitis, n = 28; ileocolic disease, n = 116; enteritis, n = 29) and were genotyped for 258 Crohn's-associated single nucleotide polymorphisms. Patients with ulcerative colitis (n = 119) were also genotyped to confirm the association of identified single nucleotide polymorphisms with small-bowel sparing, colonic pathology. MAIN OUTCOME MEASURES We investigated an association between single nucleotide polymorphisms and Crohn's disease distribution. RESULTS Single nucleotide polymorphism rs16967637 in the STAT5 gene was associated with small-bowel sparing Crohn's disease when the enteritis group was compared with either a combined colitis/ileocolic group (p = 0.025) or those with only ileocolic disease (p = 0.04). Homozygosity for the at-risk allele (C) was present in 59% of patients with sparing of the small bowel. The association of this single nucleotide polymorphism with small-bowel sparing disease persisted when patients with ulcerative colitis were compared with the group with Crohn's enteritis (p = 0.036), as well as after combining patients with ulcerative colitis with both the Crohn's colitis group (p = 0.009) and the Crohn's ileocolitis/colitis group (p = 0.00008). LIMITATIONS This study was limited by the small numbers of study subjects with isolated enteritis or colitis. CONCLUSIONS Single nucleotide polymorphism rs16967637 in the STAT5 gene was the only single nucleotide polymorphism associated with Crohn's disease without enteritis. Homozygosity for the at-risk allele demonstrated the strongest association with this phenotype. These results suggest a role for this single nucleotide polymorphism in the development of inflammatory bowel disease of the large intestine.
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Gee HY, Saisawat P, Ashraf S, Hurd TW, Vega-Warner V, Fang H, Beck BB, Gribouval O, Zhou W, Diaz KA, Natarajan S, Wiggins RC, Lovric S, Chernin G, Schoeb DS, Ovunc B, Frishberg Y, Soliman NA, Fathy HM, Goebel H, Hoefele J, Weber LT, Innis JW, Faul C, Han Z, Washburn J, Antignac C, Levy S, Otto EA, Hildebrandt F. ARHGDIA mutations cause nephrotic syndrome via defective RHO GTPase signaling. J Clin Invest 2013; 123:3243-53. [PMID: 23867502 DOI: 10.1172/jci69134] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 05/10/2013] [Indexed: 01/15/2023] Open
Abstract
Nephrotic syndrome (NS) is divided into steroid-sensitive (SSNS) and -resistant (SRNS) variants. SRNS causes end-stage kidney disease, which cannot be cured. While the disease mechanisms of NS are not well understood, genetic mapping studies suggest a multitude of unknown single-gene causes. We combined homozygosity mapping with whole-exome resequencing and identified an ARHGDIA mutation that causes SRNS. We demonstrated that ARHGDIA is in a complex with RHO GTPases and is prominently expressed in podocytes of rat glomeruli. ARHGDIA mutations (R120X and G173V) from individuals with SRNS abrogated interaction with RHO GTPases and increased active GTP-bound RAC1 and CDC42, but not RHOA, indicating that RAC1 and CDC42 are more relevant to the pathogenesis of this SRNS variant than RHOA. Moreover, the mutations enhanced migration of cultured human podocytes; however, enhanced migration was reversed by treatment with RAC1 inhibitors. The nephrotic phenotype was recapitulated in arhgdia-deficient zebrafish. RAC1 inhibitors were partially effective in ameliorating arhgdia-associated defects. These findings identify a single-gene cause of NS and reveal that RHO GTPase signaling is a pathogenic mediator of SRNS.
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Affiliation(s)
- Heon Yung Gee
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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Abstract
BACKGROUND Anal complications of Crohn's disease range from painless skin tags to debilitating fistulas that are imperfectly treated with tumor necrosis factor antagonists. The recent discovery of more than 190 single-nucleotide polymorphisms associated with Crohn's disease offers the opportunity to genetically define the severity of anal disease in Crohn's disease and possibly predict prognosis and anti-tumor necrosis factor response. OBJECTIVES This study aimed to identify single nucleotide polymorphisms associated with anal disease generally, septic anal disease specifically and the responsivity to anti-tumor necrosis factor treatment. DESIGN All patients with ileocolonic Crohn's disease were identified from our IBD registry. One hundred ninety-six Crohn's disease-related single-nucleotide polymorphisms were analyzed by the use of a custom microarray chip. Patients' response to anti-tumor necrosis factor treatment was then assessed. RESULTS One hundred sixteen patients with ileocolonic Crohn's disease were identified and assigned to septic anal disease (abscesses/fistulas, n = 35), benign anal disease (skin tags/fissures/isolated pain, n = 17), and no anal disease (n = 64) cohorts. Single-nucleotide polymorphism rs212388 negatively correlated with the presence of anal disease overall and septic disease specifically. The presence of the non-wild-type allele 'G' was protective of anal sepsis with homo- and heterozygotes having a 75% chance of no anal disease (p = 0.0001). The homozygous wild-type group had the highest risk of septic disease and included 3 of 4 patients requiring diverting ileostomies. Twenty-four patients were treated with anti-tumor necrosis factors. Nine had a beneficial response (assessed at >6 months); however, no single-nucleotide polymorphism correlated with anti-tumor necrosis factor response. Rs212388 is associated with the TAGAP molecule involved in T-cell activation. CONCLUSIONS Rs212388 most significantly correlated with the presence and severity of anal disease in ileocolonic Crohn's disease. A single copy of the risk allele was protective, whereas wild-type homozygotes had the highest risk of septic disease and stoma creation. In this select group, no single-nucleotide polymorphism was predictive of anti-tumor necrosis factor response. Mutations in TAGAP may predict a more benign form and course of anal disease in Crohn's disease.
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Londin ER, Keller MA, D'Andrea MR, Delgrosso K, Ertel A, Surrey S, Fortina P. Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor. BMC Genomics 2011; 12:464. [PMID: 21943378 PMCID: PMC3203102 DOI: 10.1186/1471-2164-12-464] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 09/26/2011] [Indexed: 11/10/2022] Open
Abstract
Background The creation of lymphoblastoid cell lines (LCLs) through Epstein-Barr virus (EBV) transformation of B-lymphocytes can result in a valuable biomaterial for cell biology research and a renewable source of DNA. While LCLs have been used extensively in cellular and genetic studies, the process of cell transformation and expansion during culturing may introduce genomic changes that may impact their use and the interpretation of subsequent genetic findings. Results We performed whole exome sequencing on a tetrad family using DNA derived from peripheral blood mononuclear cells (PBMCs) and LCLs from each individual. We generated over 4.7 GB of mappable sequence to a 125X read coverage per sample. An average of 19,354 genetic variants were identified. Comparison of the two DNA sources from each individual showed an average concordance rate of 95.69%. By lowering the variant calling parameters, the concordance rate between the paired samples increased to 99.82%. Sanger sequencing of a subset of the remaining discordant variants did confirm the presence of de novo mutations arising in LCLs. Conclusions By varying software stringency parameters, we identified 99% concordance between DNA sequences derived from the two different sources from the same donors. These results suggest that LCLs are an appropriate representation of the genetic material of the donor and suggest that EBV transformation can result in low-level generation of de novo mutations. Therefore, use of PBMC or early passage EBV-transformed cells is recommended. These findings have broad-reaching implications, as there are thousands of LCLs in public biorepositories and individual laboratories.
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Human lymphoblastoid B-cell lines reprogrammed to EBV-free induced pluripotent stem cells. Blood 2011; 118:1797-800. [PMID: 21708888 DOI: 10.1182/blood-2011-01-332064] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Generation of patient-specific induced pluripotent cells (iPSCs) holds great promise for regenerative medicine. Epstein-Barr virus immortalized lymphoblastoid B-cell lines (LCLs) can be generated from a minimal amount of blood and are banked worldwide as cellular reference material for immunologic or genetic analysis of pedigreed study populations. We report the generation of iPSCs from 2 LCLs (LCL-iPSCs) via a feeder-free episomal method using a cocktail of transcription factors and small molecules. LCL-derived iPSCs exhibited normal karyotype, expressed pluripotency markers, lost oriP/EBNA-1 episomal vectors, generated teratomas, retained donor identity, and differentiated in vitro into hematopoietic, cardiac, neural, and hepatocyte-like lineages. Significantly, although the parental LCLs express viral EBNA-1 and other Epstein-Barr virus latency-related elements for their survival, their presence was not detectable in LCL-iPSCs. Thus, reprogramming LCLs could offer an unlimited source for patient-specific iPSCs.
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Reprogramming of EBV-immortalized B-lymphocyte cell lines into induced pluripotent stem cells. Blood 2011; 118:1801-5. [PMID: 21628406 DOI: 10.1182/blood-2011-03-340620] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
EBV-immortalized B lymphocyte cell lines have been widely banked for studying a variety of diseases, including rare genetic disorders. These cell lines represent an important resource for disease modeling with the induced pluripotent stem cell (iPSC) technology. Here we report the generation of iPSCs from EBV-immortalized B-cell lines derived from multiple inherited disease patients via a nonviral method. The reprogramming method for the EBV cell lines involves a distinct protocol compared with that of patient fibroblasts. The B-cell line-derived iPSCs expressed pluripotency markers, retained the inherited mutation and the parental V(D)J rearrangement profile, and differentiated into all 3 germ layer cell types. There was no integration of the reprogramming-related transgenes or the EBV-associated genes in these iPSCs. The ability to reprogram the widely banked patient B-cell lines will offer an unprecedented opportunity to generate human disease models and provide novel drug therapies.
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Zhang J, Yin L, Liang G, Liu R, Pu Y. Detection of quinone oxidoreductase 1 (NQO1) single-nucleotide polymorphisms (SNP) related to benzene metabolism in immortalized B lymphocytes from a Chinese Han population. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2010; 73:490-498. [PMID: 20391128 DOI: 10.1080/15287390903523436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Single-nucleotide polymorphisms (SNP) in genes coding metabolizing enzymes modulate gene functions and cellular toxicity in response to chemicals. Quinone oxidoreductase 1 (NQO1) is an important detoxification enzyme involved in the catabolism of 1,4-benzoquinone (1,4-BQ), a benzene metabolite believed to be associated with bone-marrow toxicity and leukemia. Gene function was evaluated in immortalized human B lymphocytes derived from a Chinese Han population with independent genotypes at 2 NQO1 SNP sites. 1,4-Benzoquinone was incubated with these immortalized lymphocytes of differing genotypes. Among the genotypes of 2 SNP examined, cell lines with rs1800566CC showed a higher NQO1 enzymic activity after a 48 h of treatment with 10 muM 1,4-BQ, and a lower comet rate compared with cells of CT/TT genotypes. Data suggested that NQO1 rs1800566 might serve as a functional genetic marker for benzene toxicity in the Chinese Han population. The immortalized B lymphocytes derived from different populations might thus be used as a biomarker to detect functional genetic markers related to exposure to environmental chemicals.
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Affiliation(s)
- Juan Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, People's Republic of China
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Jones R. Extracting, storing and distributing DNA for a birth cohort study. Paediatr Perinat Epidemiol 2009; 23 Suppl 1:127-33. [PMID: 19490452 DOI: 10.1111/j.1365-3016.2008.01005.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Issues surrounding DNA extraction from biological samples are discussed, together with details of storage and distribution methods. The benefits of laying down immortalised cell lines are described.
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Affiliation(s)
- Richard Jones
- Centre for Child and Adolescent Health, Department of Community Based Medicine, University of Bristol, Bristol, UK.
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