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Dovrolis N, Filidou E, Kolios G. Systems biology in inflammatory bowel diseases: on the way to precision medicine. Ann Gastroenterol 2019; 32:233-246. [PMID: 31040620 PMCID: PMC6479645 DOI: 10.20524/aog.2019.0373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eirini Filidou
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Correspondence to: Prof. George Kolios, MD PhD, Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Dragana, Alexandroupolis, 68100, Greece, e-mail:
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Aatsinki SM, Elkhwanky MS, Kummu O, Karpale M, Buler M, Viitala P, Rinne V, Mutikainen M, Tavi P, Franko A, Wiesner RJ, Chambers KT, Finck BN, Hakkola J. Fasting-Induced Transcription Factors Repress Vitamin D Bioactivation, a Mechanism for Vitamin D Deficiency in Diabetes. Diabetes 2019; 68:918-931. [PMID: 30833469 PMCID: PMC6477896 DOI: 10.2337/db18-1050] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/26/2019] [Indexed: 12/19/2022]
Abstract
Low 25-hydroxyvitamin D levels correlate with the prevalence of diabetes; however, the mechanisms remain uncertain. Here, we show that nutritional deprivation-responsive mechanisms regulate vitamin D metabolism. Both fasting and diabetes suppressed hepatic cytochrome P450 (CYP) 2R1, the main vitamin D 25-hydroxylase responsible for the first bioactivation step. Overexpression of coactivator peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α), induced physiologically by fasting and pathologically in diabetes, resulted in dramatic downregulation of CYP2R1 in mouse hepatocytes in an estrogen-related receptor α (ERRα)-dependent manner. However, PGC-1α knockout did not prevent fasting-induced suppression of CYP2R1 in the liver, indicating that additional factors contribute to the CYP2R1 repression. Furthermore, glucocorticoid receptor (GR) activation repressed the liver CYP2R1, suggesting GR involvement in the regulation of CYP2R1. GR antagonist mifepristone partially prevented CYP2R1 repression during fasting, suggesting that glucocorticoids and GR contribute to the CYP2R1 repression during fasting. Moreover, fasting upregulated the vitamin D catabolizing CYP24A1 in the kidney through the PGC-1α-ERRα pathway. Our study uncovers a molecular mechanism for vitamin D deficiency in diabetes and reveals a novel negative feedback mechanism that controls crosstalk between energy homeostasis and the vitamin D pathway.
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Affiliation(s)
- Sanna-Mari Aatsinki
- Research Unit of Biomedicine, Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Admescope Ltd., Oulu, Finland
| | - Mahmoud-Sobhy Elkhwanky
- Research Unit of Biomedicine, Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Outi Kummu
- Research Unit of Biomedicine, Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Mikko Karpale
- Research Unit of Biomedicine, Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Marcin Buler
- Research Unit of Biomedicine, Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Pirkko Viitala
- Research Unit of Biomedicine, Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | | | - Maija Mutikainen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pasi Tavi
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Andras Franko
- Institute of Vegetative Physiology, Medical Faculty, University of Köln, Köln, Germany
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Rudolf J Wiesner
- Institute of Vegetative Physiology, Medical Faculty, University of Köln, Köln, Germany
| | - Kari T Chambers
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Brian N Finck
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Jukka Hakkola
- Research Unit of Biomedicine, Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
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53
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Tong R, Zhang L, Hu C, Chen X, Song Q, Lou K, Tang X, Chen Y, Gong X, Gao Y, Wen W. An Automated and Miniaturized Rotating-Disk Device for Rapid Nucleic Acid Extraction. MICROMACHINES 2019; 10:E204. [PMID: 30909465 PMCID: PMC6471407 DOI: 10.3390/mi10030204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/08/2019] [Accepted: 03/20/2019] [Indexed: 11/20/2022]
Abstract
The result of molecular diagnostic and detection greatly dependent on the quality and integrity of the isolated nucleic acid. In this work, we developed an automated miniaturized nucleic acid extraction device based on magnetic beads method, consisting of four components including a sample processing disc and its associated rotary power output mechanism, a pipetting module, a magnet module and an external central controller to enable a customizable and automated robust nucleic acid sample preparation. The extracted nucleic acid using 293T cells were verified using real-time polymerase chain reaction (PCR) and the data implies a comparable efficiency to a manual process, with the advantages of performing a flexible, time-saving (~10 min), and simple nucleic acid sample preparation.
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Affiliation(s)
- Rui Tong
- The Nano Science and Technology (NSNT) Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Lijuan Zhang
- Shenzhen Shineway Hi-Tech Co., Ltd., Shenzhen 518112, China.
| | - Chuandeng Hu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Xuee Chen
- The Nano Science and Technology (NSNT) Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Qi Song
- Guangzhou HKUST Fok Ying Tung Research Institute, Nansha, Guangzhou 511458, China.
| | - Kai Lou
- Shenzhen Shineway Hi-Tech Co., Ltd., Shenzhen 518112, China.
| | - Xin Tang
- Guangzhou HKUST Fok Ying Tung Research Institute, Nansha, Guangzhou 511458, China.
| | - Yongsheng Chen
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Xiuqing Gong
- Materials Genome Institute, University of Shanghai, Shanghai 200444, China.
| | - Yibo Gao
- Shenzhen Shineway Hi-Tech Co., Ltd., Shenzhen 518112, China.
| | - Weijia Wen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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54
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Oberacker P, Stepper P, Bond DM, Höhn S, Focken J, Meyer V, Schelle L, Sugrue VJ, Jeunen GJ, Moser T, Hore SR, von Meyenn F, Hipp K, Hore TA, Jurkowski TP. Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation. PLoS Biol 2019; 17:e3000107. [PMID: 30629605 PMCID: PMC6343928 DOI: 10.1371/journal.pbio.3000107] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/23/2019] [Indexed: 01/10/2023] Open
Abstract
Current molecular biology laboratories rely heavily on the purification and manipulation of nucleic acids. Yet, commonly used centrifuge- and column-based protocols require specialised equipment, often use toxic reagents, and are not economically scalable or practical to use in a high-throughput manner. Although it has been known for some time that magnetic beads can provide an elegant answer to these issues, the development of open-source protocols based on beads has been limited. In this article, we provide step-by-step instructions for an easy synthesis of functionalised magnetic beads, and detailed protocols for their use in the high-throughput purification of plasmids, genomic DNA, RNA and total nucleic acid (TNA) from a range of bacterial, animal, plant, environmental and synthetic sources. We also provide a bead-based protocol for bisulfite conversion and size selection of DNA and RNA fragments. Comparison to other methods highlights the capability, versatility, and extreme cost-effectiveness of using magnetic beads. These open-source protocols and the associated webpage (https://bomb.bio) can serve as a platform for further protocol customisation and community engagement. This Community Page article presents open-source nucleic acid purification and handling protocols based on functionalised magnetic beads, with the aim of transforming life science research practice and its economics.
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Affiliation(s)
- Phil Oberacker
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Peter Stepper
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Donna M. Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Sven Höhn
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jule Focken
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Vivien Meyer
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Luca Schelle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | | | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Tim Moser
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Ferdinand von Meyenn
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom and Department of Medical and Molecular Medicine, Kings College London, Guys Hospital, London, United Kingdom
| | - Katharina Hipp
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Timothy A. Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- * E-mail: (TPJ); (TAH)
| | - Tomasz P. Jurkowski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail: (TPJ); (TAH)
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55
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Niibo M, Shirouchi B, Umegatani M, Morita Y, Ogawa A, Sakai F, Kadooka Y, Sato M. Probiotic Lactobacillus gasseri SBT2055 improves insulin secretion in a diabetic rat model. J Dairy Sci 2018; 102:997-1006. [PMID: 30471910 DOI: 10.3168/jds.2018-15203] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/18/2018] [Indexed: 01/16/2023]
Abstract
The probiotic Lactobacillus gasseri SBT2055 (LG2055) has a protective effect against metabolic syndrome in rats and humans. Metabolic syndrome increases the risk of type 2 diabetes mellitus. In this study, Goto-Kakizaki rats were used as a diabetic model and fed diets containing LG2055-fermented or nonfermented skim milk for 4 wk. Indices of diabetes such as blood glucose levels, serum glucagon levels, plasma levels of insulin, C-peptide, and glucagon-like peptide-1, tissue glycogen contents, and pancreatic mRNA levels were measured. The plasma C-peptide levels and pancreatic mRNA levels of insulin genes (Ins1 and Ins2) and Pdx1 (a transcriptional factor of insulin genes) were increased in LG2055 diet-fed rats. The increase in insulin secretion corresponded to an improvement in serum and pancreatic inflammatory status, associated with decreases in serum levels of serum amyloid P and pancreatic levels of granulocyte colony-stimulating factor. Insulin resistance in Goto-Kakizaki rats was ameliorated by increased glycogen storage in the liver and quadriceps femoris muscles and decreased serum free fatty acid levels. This improvement may be related to the increased cecal production of short-chain fatty acids. In conclusion, dietary LG2055 improved insulin secretion in diabetic rats by improving the inflammatory status in the pancreas and serum.
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Affiliation(s)
- M Niibo
- Laboratory of Nutrition Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - B Shirouchi
- Laboratory of Nutrition Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - M Umegatani
- Laboratory of Nutrition Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Y Morita
- Laboratory of Nutrition Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - A Ogawa
- Milk Science Research Institute, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe, Saitama 350-1165, Japan
| | - F Sakai
- Milk Science Research Institute, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe, Saitama 350-1165, Japan
| | - Y Kadooka
- Milk Science Research Institute, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe, Saitama 350-1165, Japan
| | - M Sato
- Laboratory of Nutrition Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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56
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Inactivation of NUPR1 promotes cell death by coupling ER-stress responses with necrosis. Sci Rep 2018; 8:16999. [PMID: 30451898 PMCID: PMC6242935 DOI: 10.1038/s41598-018-35020-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
It was already described that genetic inhibition of NUPR1 induces tumor growth arrest. In this paper we studied the metabolism changes after NUPR1 downregulation in pancreatic cancer cells, which results in a significant decrease of OXPHOS activity with a concomitant lower ATP production which precedes the necrotic cell death. We demonstrated that NUPR1 downregulation induces a mitochondrial failure with a loss of the mitochondrial membrane potential, a strong increase in ROS production and a concomitant relocalization of mitochondria to the vicinity of the endoplasmic reticulum (ER). In addition, the transcriptomic analysis of NUPR1-deficient cells shows a decrease in the expression of some ER stress response-associated genes. Indeed, in ER stressors-treated cells with thapsigargin, brefeldin A or tunicamycin, a greater increase in necrosis and decrease of ATP content was observed in NUPR1-defficent cells. Finally, in vivo experiments, using acute pancreatitis which induces ER stress as well as NUPR1 activation, we observed that NUPR1 expression protects acinar cells from necrosis in mice. Importantly, we also report that the cell death observed after knocking-down NUPR1 expression is completely reversed by incubation with Necrostatin-1, but not by inhibiting caspase activity with Z-VAD-FMK. Altogether, these data enable us to describe a model in which inactivation of NUPR1 in pancreatic cancer cells results in an ER stress that induces a mitochondrial malfunction, a deficient ATP production and, as consequence, the cell death mediated by a programmed necrosis.
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57
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Gu W, Miller S, Chiu CY. Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018; 14:319-338. [PMID: 30355154 DOI: 10.1146/annurev-pathmechdis-012418-012751] [Citation(s) in RCA: 675] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its advent in 2004, and it has emerged as an enabling technological platform for the detection and taxonomic characterization of microorganisms in clinical samples from patients. This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations. The review covers ( a) next-generation sequencing technologies and common platforms, ( b) next-generation sequencing assay workflows in the clinical microbiology laboratory, ( c) bioinformatics analysis of metagenomic next-generation sequencing data, ( d) validation and use of metagenomic next-generation sequencing for diagnosing infectious diseases, and ( e) significant case reports and studies in this area. Next-generation sequencing is a new technology that has the promise to enhance our ability to diagnose, interrogate, and track infectious diseases.
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Affiliation(s)
- Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA; .,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California 94107, USA
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58
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Peterson SW, Logrieco A. Ribosomal Rna Sequence Variation Among Interfertile Strains of SomeGibberellaSpecies. Mycologia 2018. [DOI: 10.1080/00275514.1991.12026028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Stephen W. Peterson
- Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, Illinois 61604
| | - Antonio Logrieco
- Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, Illinois 61604
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59
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Marais GJ, Wingfield MJ, Viljoen CD, Wingfield BD. A new ophiostomatoid genus from Protea infructescences. Mycologia 2018. [DOI: 10.1080/00275514.1998.12026890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Gert J. Marais
- Department of Microbiology and Biochemistry, University of the Orange Free State, P. O. Box 339, Bloemfontein, 9300, South Africa
| | - Michael J. Wingfield
- Department of Microbiology and Biochemistry, University of the Orange Free State, P. O. Box 339, Bloemfontein, 9300, South Africa
| | - Christopher D. Viljoen
- Department of Microbiology and Biochemistry, University of the Orange Free State, P. O. Box 339, Bloemfontein, 9300, South Africa
| | - Brenda D. Wingfield
- Department of Microbiology and Biochemistry, University of the Orange Free State, P. O. Box 339, Bloemfontein, 9300, South Africa
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60
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Comparison of various RNA extraction methods, cDNA preparation and isolation of calmodulin gene from a highly melanized isolate of apple leaf blotch fungus Marssonina coronaria. J Microbiol Methods 2018; 151:7-15. [DOI: 10.1016/j.mimet.2018.05.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/22/2018] [Accepted: 05/28/2018] [Indexed: 11/19/2022]
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61
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Asencio C, Chatterjee A, Hentze MW. Silica-based solid-phase extraction of cross-linked nucleic acid-bound proteins. Life Sci Alliance 2018; 1:e201800088. [PMID: 30035255 PMCID: PMC6054301 DOI: 10.26508/lsa.201800088] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The 2C method allows the rapid and straightforward isolation of nucleic acid–protein complexes, greatly simplifying downstream applications for the study of DNA– and RNA–protein interactions. Proteins interact with nucleic acids to regulate cellular functions. The study of these regulatory interactions is often hampered by the limited efficiency of current protocols to isolate the relevant nucleic acid–protein complexes. In this report, we describe a rapid and simple procedure to highly enrich cross-linked nucleic acid–bound proteins, referred to as “2C” for “complex capture.” This method is based on the observation that silica matrix–based columns used for nucleic acid purification also effectively retain UV cross-linked nucleic acid–protein complexes. As a proof of principle, 2C was used to isolate RNA-bound proteins from yeast and mammalian Huh7 cells. The 2C method makes RNA labelling redundant, and specific RNA–protein interactions can be observed and validated by Western blotting. RNA–protein complexes isolated by 2C can subsequently be immunoprecipitated, showing that 2C is in principle compatible with sensitive downstream applications. We suggest that 2C can dramatically simplify the study of nucleic acid–protein interactions and benefit researchers in the fields of DNA and RNA biology.
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Affiliation(s)
- Claudio Asencio
- European Molecular Biology Laboratory, Heidelberg, Germany.,Centro Andaluz de Biología del Desarrollo, Universidad Pablo Olavide, Sevilla, Spain
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62
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Griesmann M, Chang Y, Liu X, Song Y, Haberer G, Crook MB, Billault-Penneteau B, Lauressergues D, Keller J, Imanishi L, Roswanjaya YP, Kohlen W, Pujic P, Battenberg K, Alloisio N, Liang Y, Hilhorst H, Salgado MG, Hocher V, Gherbi H, Svistoonoff S, Doyle JJ, He S, Xu Y, Xu S, Qu J, Gao Q, Fang X, Fu Y, Normand P, Berry AM, Wall LG, Ané JM, Pawlowski K, Xu X, Yang H, Spannagl M, Mayer KFX, Wong GKS, Parniske M, Delaux PM, Cheng S. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science 2018; 361:science.aat1743. [DOI: 10.1126/science.aat1743] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/16/2018] [Indexed: 12/20/2022]
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63
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Kinnunen SM, Tölli M, Välimäki MJ, Gao E, Szabo Z, Rysä J, Ferreira MPA, Ohukainen P, Serpi R, Correia A, Mäkilä E, Salonen J, Hirvonen J, Santos HA, Ruskoaho H. Cardiac Actions of a Small Molecule Inhibitor Targeting GATA4-NKX2-5 Interaction. Sci Rep 2018; 8:4611. [PMID: 29545582 PMCID: PMC5854571 DOI: 10.1038/s41598-018-22830-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/23/2018] [Indexed: 02/07/2023] Open
Abstract
Transcription factors are fundamental regulators of gene transcription, and many diseases, such as heart diseases, are associated with deregulation of transcriptional networks. In the adult heart, zinc-finger transcription factor GATA4 is a critical regulator of cardiac repair and remodelling. Previous studies also suggest that NKX2-5 plays function role as a cofactor of GATA4. We have recently reported the identification of small molecules that either inhibit or enhance the GATA4–NKX2-5 transcriptional synergy. Here, we examined the cardiac actions of a potent inhibitor (3i-1000) of GATA4–NKX2-5 interaction in experimental models of myocardial ischemic injury and pressure overload. In mice after myocardial infarction, 3i-1000 significantly improved left ventricular ejection fraction and fractional shortening, and attenuated myocardial structural changes. The compound also improved cardiac function in an experimental model of angiotensin II -mediated hypertension in rats. Furthermore, the up-regulation of cardiac gene expression induced by myocardial infarction and ischemia reduced with treatment of 3i-1000 or when micro- and nanoparticles loaded with 3i-1000 were injected intramyocardially or intravenously, respectively. The compound inhibited stretch- and phenylephrine-induced hypertrophic response in neonatal rat cardiomyocytes. These results indicate significant potential for small molecules targeting GATA4–NKX2-5 interaction to promote myocardial repair after myocardial infarction and other cardiac injuries.
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Affiliation(s)
- Sini M Kinnunen
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, Helsinki, Finland.,Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, Oulu, Finland
| | - Marja Tölli
- Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, Oulu, Finland
| | - Mika J Välimäki
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, Helsinki, Finland.,Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, Oulu, Finland
| | - Erhe Gao
- Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, United States of America
| | - Zoltan Szabo
- Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, Oulu, Finland
| | - Jaana Rysä
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mónica P A Ferreira
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Pauli Ohukainen
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
| | - Raisa Serpi
- Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, Oulu, Finland
| | - Alexandra Correia
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ermei Mäkilä
- Laboratory of Industrial Physics, Department of Physics and Astronomy, University of Turku, Turku, Finland
| | - Jarno Salonen
- Laboratory of Industrial Physics, Department of Physics and Astronomy, University of Turku, Turku, Finland
| | - Jouni Hirvonen
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Hélder A Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Heikki Ruskoaho
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, Helsinki, Finland. .,Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, Oulu, Finland.
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64
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Mileo AM, Fanuele M, Battaglia F, Scambia G, Benedetti-Panici C, Mattei E, Mancuso S, Delpino A. Preliminary evaluation of HER-2/neu oncogene and epidermal growth factor receptor expression in normal and neoplastic human ovaries. Int J Biol Markers 2018; 7:114-8. [PMID: 1634822 DOI: 10.1177/172460089200700208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The HER-2/neu oncogene (a member of the Erb-like oncogene family) is distinct from but closely related to the c-erb B gene which encodes the epidermal growth factor receptor (EGFr). HER-2/neu gene amplification was found in a large number of mammary carcinomas and there was a strong correlation between this phenomenon and poor prognosis. In our study HER-2/neu oncogene expression was determined in 16 malignant ovarian tumors, 2 ovarian lymphomas and 5 normal ovaries. The HER-2/neu gene was found both in normal ovaries and malignant tumors, without any apparent difference among the various histological types. In all the specimens examined, HER-2/neu expression did not seem to be related to EGF binding capacity.
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Affiliation(s)
- A M Mileo
- Regina Elena Institute for Cancer Research, Roma, Italy
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65
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Ribar A, Huber SE, Smiałek MA, Tanzer K, Neustetter M, Schürmann R, Bald I, Denifl S. Hydroperoxyl radical and formic acid formation from common DNA stabilizers upon low energy electron attachment. Phys Chem Chem Phys 2018; 20:5578-5585. [PMID: 29410988 DOI: 10.1039/c7cp07697e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
2-Amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) and ethylenediaminetetraacetic acid (EDTA) are key components of biological buffers and are frequently used as DNA stabilizers in irradiation studies. Such surface or liquid phase studies are done with the aim to understand the fundamental mechanisms of DNA radiation damage and to improve cancer radiotherapy. When ionizing radiation is used, abundant secondary electrons are formed during the irradiation process, which are able to attach to the molecular compounds present on the surface. In the present study we experimentally investigate low energy electron attachment to TRIS and methyliminodiacetic acid (MIDA), an analogue of EDTA, supported by quantum chemical calculations. The most prominent dissociation channel for TRIS is through hydroperoxyl radical formation, whereas the dissociation of MIDA results in the formation of formic and acetic acid. These compounds are well-known to cause DNA modifications, like strand breaks. The present results indicate that buffer compounds may not have an exclusive protecting effect on DNA as suggested previously.
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Affiliation(s)
- Anita Ribar
- Institute for Ion Physics and Applied Physics and Center of Molecular Biosciences Innsbruck, Leopold Franzens University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.
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66
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Kebede AZ, Johnston A, Schneiderman D, Bosnich W, Harris LJ. Transcriptome profiling of two maize inbreds with distinct responses to Gibberella ear rot disease to identify candidate resistance genes. BMC Genomics 2018; 19:131. [PMID: 29426290 PMCID: PMC5807830 DOI: 10.1186/s12864-018-4513-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/31/2018] [Indexed: 11/27/2022] Open
Abstract
Background Gibberella ear rot (GER) is one of the most economically important fungal diseases of maize in the temperate zone due to moldy grain contaminated with health threatening mycotoxins. To develop resistant genotypes and control the disease, understanding the host-pathogen interaction is essential. Results RNA-Seq-derived transcriptome profiles of fungal- and mock-inoculated developing kernel tissues of two maize inbred lines were used to identify differentially expressed transcripts and propose candidate genes mapping within GER resistance quantitative trait loci (QTL). A total of 1255 transcripts were significantly (P ≤ 0.05) up regulated due to fungal infection in both susceptible and resistant inbreds. A greater number of transcripts were up regulated in the former (1174) than the latter (497) and increased as the infection progressed from 1 to 2 days after inoculation. Focusing on differentially expressed genes located within QTL regions for GER resistance, we identified 81 genes involved in membrane transport, hormone regulation, cell wall modification, cell detoxification, and biosynthesis of pathogenesis related proteins and phytoalexins as candidate genes contributing to resistance. Applying droplet digital PCR, we validated the expression profiles of a subset of these candidate genes from QTL regions contributed by the resistant inbred on chromosomes 1, 2 and 9. Conclusion By screening global gene expression profiles for differentially expressed genes mapping within resistance QTL regions, we have identified candidate genes for gibberella ear rot resistance on several maize chromosomes which could potentially lead to a better understanding of Fusarium resistance mechanisms. Electronic supplementary material The online version of this article (10.1186/s12864-018-4513-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aida Z Kebede
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.,Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Anne Johnston
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Danielle Schneiderman
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Whynn Bosnich
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Linda J Harris
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
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67
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Feng R, Li L, Li B, Li J, Peng D, Yu Y, Mu Q, Zhao N, Yu X, Wang Z. A small-molecule with a large two-photon absorption cross-section serves as a membrane-permeable ribonucleic acid (RNA) probe for live cell imaging. NEW J CHEM 2018. [DOI: 10.1039/c8nj02425a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DMI could light up the RNA of the nucleus and the cytoplasm in living systems, which not only exhibits larger two-photon absorption cross-sections (981 GM), but also displays high-permeability to plasma membranes of vigorous cells.
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68
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Mäkelä MR, Hildén K. Efficient Extraction Method for High Quality Fungal RNA from Complex Lignocellulosic Substrates. Methods Mol Biol 2018; 1775:69-73. [PMID: 29876809 DOI: 10.1007/978-1-4939-7804-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we describe an efficient and reproducible method for the extraction of fungal RNA from complex lignocellulose containing materials. The fungal cells are snap-frozen and disrupted in chaotropic guanidinium thiocyanate buffer, after which the extracted RNA is isolated by using CsCl gradient ultracentrifugation. By lowering the pH of the extraction buffer, the procedure is also suitable for sample materials rich in humic acids. The method results in high quantity and quality RNA that is separated from endogenous contaminants (e.g., RNases) and substances derived from plant biomass (e.g., colored aromatic compounds). In addition, no further steps such as DNase treatment are needed. The extracted RNA is highly suitable for downstream gene expression analyses such as RNA sequencing.
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Affiliation(s)
- Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
| | - Kristiina Hildén
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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69
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Liu X, Zeng Z, Zhao L, Xiao W, Chen P. Changes in inflammatory and oxidative stress factors and the protein synthesis pathway in injured skeletal muscle after contusion. Exp Ther Med 2017; 15:2196-2202. [PMID: 29434825 DOI: 10.3892/etm.2017.5625] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022] Open
Abstract
Injury of skeletal muscle, and particularly mechanically-induced damage, including contusion injury, frequently occurs in contact sports as well as in sports with accidental contact. Although the mechanisms of skeletal muscle regeneration are well understood, those involved in muscle contusion are not. A total of 40 male mice were randomly divided into control (n=8) and muscle contusion (n=32) groups. A muscle contusion model was established by weight-drop injury. Subsequently, the gastrocnemius muscles in the two groups were harvested at different times (1, 3, 7 and 14 days) post-injury. The changes in skeletal muscle morphology were assessed by hematoxylin and eosin (H&E) stains. Furthermore, quantitative polymerase chain reaction and western blotting were used to analyze inflammatory cytokines, oxidative stress factors and the Akt/mechanistic target of rapamycin (mTOR) pathway. The results revealed that pro-inflammatory cytokines [tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and interferon-γ (IFN-γ)] increased significantly at day 1 and 3 and still exhibited high levels of expression at days 7 and 14 (except IL-6) post-injury. Additionally, the anti-inflammatory cytokine IL-10 increased significantly at 1, 3 and 7 days and reached its peak levels at 7 days post-injury. It was revealed that gp91phox mRNA increased significantly at all time points and gp91phox protein increased significantly at day 3 post-injury. Furthermore, it was observed that p-Akt/Akt increased significantly at 1 day post-injury. P-mTOR/mTOR increased significantly at day 1 and 7, and p-p70s6k/p70s6k and P-4EBP1/4EBP1 increased significantly at 1, 3, 7 and 14 days post-injury. These results indicate that inflammatory and oxidative stress factors and the Akt/mTOR pathway may serve important roles in the regeneration of muscle contusion. In addition, certain inflammatory factors and oxidative stress factors maintained high levels of expression at 14 days after injury, indicating that the healing process of muscle was still not fully achieved at this time.
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Affiliation(s)
- Xiaoguang Liu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, P.R. China
| | - Zhigang Zeng
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, P.R. China.,College of Physical Education, Jinggangshan University, Ji'an, Jiangxi 343009, P.R. China
| | - Linlin Zhao
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, P.R. China
| | - Weihua Xiao
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, P.R. China
| | - Peijie Chen
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, P.R. China
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70
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Isegawa Y, Okuno Y. Analysis of the glycoproteins of Seoul orthohantavirus strain B1 associated with fusion activity. Arch Virol 2017; 163:419-425. [PMID: 29101537 DOI: 10.1007/s00705-017-3623-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/28/2017] [Indexed: 11/29/2022]
Abstract
We analyzed two virus variants (S1 and L1) from Seoul orthohantavirus strain B1. Strain B1 produces large opaque plaques when plated on Vero E6 cell monolayers. However, although the L1 variant produced the large opaque plaques common to the strain, the variant S1 produced small clear ones on Vero E6 cells. Five days after Vero E6 cells were infected with the S1 variant, polykaryons formed spontaneously. However, the cells infected with the L1 variant did not show the formation of syncytia. An analysis of the pH dependency of the cell fusion demonstrated that the L1 variant could induce cell fusion, but only at a pH that was 0.2 units lower than the pH at which the S1 variant induced it. Sequencing of the M genome segment of the two virus variants revealed amino acid substitutions at 4 positions in the Gn and Gc gene products of the S1 variant. Two of these substitutions occurred in the extracellular domain of Gn and changed the charge of the protein. Our findings suggest that these amino acid substitutions caused the S1 variant Gn protein to induce fusion at an elevated pH.
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Affiliation(s)
- Yuji Isegawa
- Department of Food Sciences and Nutrition, School of Human Environmental Sciences, Mukogawa Women's University, Nishinomiya, Hyogo, 663-8558, Japan.
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71
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Chang TS, Liu CW, Lin YL, Li CY, Wang AZ, Chien MW, Wang CS, Lai CC. Mapping and comparative proteomic analysis of the starch biosynthetic pathway in rice by 2D PAGE/MS. PLANT MOLECULAR BIOLOGY 2017; 95:333-343. [PMID: 28887709 DOI: 10.1007/s11103-017-0652-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 08/16/2017] [Indexed: 05/16/2023]
Abstract
Our results not only provide a comprehensive overview of the starch biosynthetic pathway in the developing endosperm but also reveal some important protein markers that regulate the synthesis of starch. In human diets, rice (Oryza sativa L.) is an important source of starch, a substantial amount of which is accumulated in developing endosperm. A better understanding of the complicated pathways involved in starch biosynthesis is needed to improve the yield and quality of rice and other cereal crops through breeding. One pure line rice mutant, SA0419, was induced from a wild-type rice, TNG67, by sodium azide mutagenesis; therefore, TNG67 and SA0419 share the same genetic background. SA0419 is, however, a unique glutinous rice with a lower amylose content (8%) than that of TNG67 (20%), and the grains of SA0419 develop earlier and faster than those of TNG67. In this study, we used a comparative proteomic analysis to identify the differentially expressed proteins that may explain the differences in starch biosynthesis and the characteristics of TNG67 and SA0419. A gel-based proteomic approach was applied to profile the expressed proteome in the developing endosperm of these two rice varieties by nano-LC/MS/MS. Several over-expressed proteins were found in SA0419, such as plastidial ADP-glucose pyrophosphorylase (AGPase), phosphoglucomutase (PGM), pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP), 6-phosphofructokinase (PFK), pyruvate phosphate dikinase (PPDK), starch branching enzymes (SBE) and starch debranching enzyme (SDBE), with those proteins mainly being involved in the pathways of starch metabolism and PPDK-mediated gluconeogenesis. Those over-expressed enzymes may contribute to the relatively early development, similar starch accumulation and rapid grain filling of SA0419 as compared with TNG67. This study provides a detailed biochemical description of starch biosynthesis and related information regarding a unique starch mutant that may assist future research efforts to improve the yield and quality of grain and starch in rice through breeding.
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Affiliation(s)
- Tao-Shan Chang
- Institute of Molecular Biology, National Chung Hsing University, No. 250, Kuo-Kuang Road, Taichung, 40227, Taiwan, Republic of China
| | - Chih-Wei Liu
- Institute of Molecular Biology, National Chung Hsing University, No. 250, Kuo-Kuang Road, Taichung, 40227, Taiwan, Republic of China
| | - Yu-Ling Lin
- Department of Agronomy, National Chung Hsing University, 250, Kuo-Kuang Rd., Taichung, Taiwan, Republic of China
| | - Chao-Yi Li
- Institute of Molecular Biology, National Chung Hsing University, No. 250, Kuo-Kuang Road, Taichung, 40227, Taiwan, Republic of China
| | - Arthur Z Wang
- Department of Agronomy, National Chung Hsing University, 250, Kuo-Kuang Rd., Taichung, Taiwan, Republic of China
| | - Min-Wei Chien
- Institute of Molecular Biology, National Chung Hsing University, No. 250, Kuo-Kuang Road, Taichung, 40227, Taiwan, Republic of China
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung Hsing University, 250, Kuo-Kuang Rd., Taichung, Taiwan, Republic of China.
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, No. 250, Kuo-Kuang Road, Taichung, 40227, Taiwan, Republic of China.
- Graduate institute of Chinese Medical Science, China Medical University, Taichung, 40402, Taiwan, Republic of China.
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72
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Suriyasak C, Harano K, Tanamachi K, Matsuo K, Tamada A, Iwaya-Inoue M, Ishibashi Y. Reactive oxygen species induced by heat stress during grain filling of rice (Oryza sativa L.) are involved in occurrence of grain chalkiness. JOURNAL OF PLANT PHYSIOLOGY 2017; 216:52-57. [PMID: 28575747 DOI: 10.1016/j.jplph.2017.05.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
Heat stress during grain filling increases rice grain chalkiness due to increased activity of α-amylase, which hydrolyzes starch. In rice and barley seeds, reactive oxygen species (ROS) produced after imbibition induce α-amylase activity via regulation of gibberellin (GA) and abscisic acid (ABA) levels during seed germination. Here, we examined whether ROS is involved in induction of grain chalkiness by α-amylase in developing rice grains under heat stress. To elucidate the role of ROS in grain chalkiness, we grew post-anthesis rice plants (Oryza sativa L. cv. Koshihikari) under control (25°C) or heat stress (30°C) conditions with or without antioxidant (dithiothreitol) treatment. The developing grains were analyzed for expression of NADPH oxidases, GA biosynthesis genes (OsGA3ox1, OsGA20ox1), ABA catabolism genes (OsABA8'OH1, OsABA8'OH2) and an α-amylase gene (OsAmy3E), endogenous H2O2 content and the grain quality. In grains exposed to heat stress, the expression of NADPH oxidase genes (especially, OsRbohB, OsRbohD, OsRbohF and OsRbohI) and the ROS content increased. Heat stress also increased the expression of OsGA3ox1, OsGA20ox1, OsABA8'OH1, OsABA8'OH2 and OsAmy3E. On the other hand, dithiothreitol treatment reduced the effects of heat stress on the expression of these genes and significantly reduced grain chalkiness induced by heat stress. These results suggest that, similar to cereal seed germination mechanism, ROS produced under heat stress is involved in α-amylase induction in maturating rice grains through GA/ABA metabolism, and consequently caused grain chalkiness.
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Affiliation(s)
- Chetphilin Suriyasak
- Laboratory of Crop Science, Department of Bioresource Science, School of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Keisuke Harano
- Laboratory of Crop Science, Department of Bioresource Science, School of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Koichiro Tanamachi
- Laboratory of Crop Science, Department of Bioresource Science, School of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Kazuhiro Matsuo
- Laboratory of Crop Science, Department of Bioresource Science, School of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Aina Tamada
- Laboratory of Crop Science, Department of Bioresource Science, School of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Mari Iwaya-Inoue
- Laboratory of Crop Science, Department of Bioresource Science, School of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Yushi Ishibashi
- Laboratory of Crop Science, Department of Bioresource Science, School of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan.
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73
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Differential Innate Immune Signaling in Macrophages by Wild-Type Vaccinia Mature Virus and a Mutant Virus with a Deletion of the A26 Protein. J Virol 2017; 91:JVI.00767-17. [PMID: 28659486 DOI: 10.1128/jvi.00767-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/23/2017] [Indexed: 12/13/2022] Open
Abstract
The Western Reserve (WR) strain of mature vaccinia virus contains an A26 envelope protein that mediates virus binding to cell surface laminin and subsequent endocytic entry into HeLa cells. Removal of the A26 protein from the WR strain mature virus generates a mutant, WRΔA26, that enters HeLa cells through plasma membrane fusion. Here, we infected murine bone marrow-derived macrophages (BMDM) with wild-type strain WR and the WRΔA26 mutant and analyzed viral gene expression and cellular innate immune signaling. In contrast to previous studies, in which both HeLa cells infected with WR and HeLa cells infected with WRΔA26 expressed abundant viral late proteins, we found that WR expressed much less viral late protein than WRΔA26 in BMDM. Microarray analysis of the cellular transcripts in BMDM induced by virus infection revealed that WR preferentially activated type 1 interferon receptor (IFNAR)-dependent signaling but WRΔA26 did not. We consistently detected a higher level of soluble beta interferon secretion and phosphorylation of the STAT1 protein in BMDM infected with WR than in BMDM infected with WRΔA26. When IFNAR-knockout BMDM were infected with WR, late viral protein expression increased, confirming that IFNAR-dependent signaling was differentially induced by WR and, in turn, restricted viral late gene expression. Finally, wild-type C57BL/6 mice were more susceptible to mortality from WRΔA26 infection than to that from WR infection, whereas IFNAR-knockout mice were equally susceptible to WR and WRΔA26 infection, demonstrating that the ability of WRΔA26 to evade IFNAR signaling has an important influence on viral pathogenesis in vivoIMPORTANCE The vaccinia virus A26 protein was previously shown to mediate virus attachment and to regulate viral endocytosis. Here, we show that infection with strain WR induces a robust innate immune response that activates type 1 interferon receptor (IFNAR)-dependent cellular genes in BMDM, whereas infection with the WRΔA26 mutant does not. We further demonstrated that the differential activation of IFNAR-dependent cellular signaling between WR and WRΔA26 not only is important for differential host restriction in BMDM but also is important for viral virulence in vivo Our study reveals a new property of WRΔA26, which is in regulating host antiviral innate immunity in vitro and in vivo.
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74
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Targeted Isolation and Characterization of T-DNA Mutants Defective in Photorespiration. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1653:105-124. [PMID: 28822129 DOI: 10.1007/978-1-4939-7225-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Transfer DNA (T-DNA) insertional lines have facilitated reverse genetic approaches in plant science and considerably accelerated the functional characterization of genes. Typically, online databases of mutant collections are searched for suitable mutant alleles of the gene of interest (GOI). Before such lines can be characterized physiologically, the genotype of the respective mutant has to be verified followed by the quantitative examination of downstream effects on the levels of the respective mRNA and the encoded protein. Here, we describe a typical workflow for the identification of photorespiratory mutants followed by phenotypic characterization according to growth under different conditions, photosynthesis on the levels of chlorophyll a fluorescence and gas exchange, and metabolite analysis.
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75
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Resnyk CW, Carré W, Wang X, Porter TE, Simon J, Le Bihan-Duval E, Duclos MJ, Aggrey SE, Cogburn LA. Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ. BMC Genomics 2017; 18:626. [PMID: 28814270 PMCID: PMC5559791 DOI: 10.1186/s12864-017-4035-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 08/08/2017] [Indexed: 11/10/2022] Open
Abstract
Background Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today’s broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens. Methods We used the Del-Mar 14 K Chicken Integrated Systems microarray to take time-course snapshots of global gene transcription in abdominal fat of juvenile [1-11 weeks of age (wk)] chickens divergently selected on bodyweight at two ages (8 and 36 wk). Further, a RNA sequencing analysis was completed on the same abdominal fat samples taken from high-growth (HG) and low-growth (LG) cockerels at 7 wk, the age with the greatest divergence in body weight (3.2-fold) and visceral fatness (19.6-fold). Results Time-course microarray analysis revealed 312 differentially expressed genes (FDR ≤ 0.05) as the main effect of genotype (HG versus LG), 718 genes in the interaction of age and genotype, and 2918 genes as the main effect of age. The RNA sequencing analysis identified 2410 differentially expressed genes in abdominal fat of HG versus LG chickens at 7 wk. The HG chickens are fatter and over-express numerous genes that support higher rates of visceral adipogenesis and lipogenesis. In abdominal fat of LG chickens, we found higher expression of many genes involved in hemostasis, energy catabolism and endocrine signaling, which likely contribute to their leaner phenotype and slower growth. Many transcription factors and their direct target genes identified in HG and LG chickens could be involved in their divergence in adiposity and growth rate. Conclusions The present analyses of the visceral fat transcriptome in chickens divergently selected for a large difference in growth rate and abdominal fatness clearly demonstrate that abdominal fat is a very dynamic metabolic and endocrine organ in the chicken. The HG chickens overexpress many transcription factors and their direct target genes, which should enhance in situ lipogenesis and ultimately adiposity. Our observation of enhanced expression of hemostasis and endocrine-signaling genes in diminished abdominal fat of LG cockerels provides insight into genetic mechanisms involved in divergence of abdominal fatness and somatic growth in avian and perhaps mammalian species, including humans. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4035-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C W Resnyk
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | - W Carré
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.,Laboratoire de Génétique Moléculaire et Génomique, CHU Pontchaillou, 35033, Rennes, France
| | - X Wang
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.,Department of Biological Sciences, Tennessee State University, Nashville, TN, 37209, USA
| | - T E Porter
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - J Simon
- UR83 Recherches Avicoles, Institut National de la Recherche Agronomique (INRA), F-37380, Nouzilly, France
| | - E Le Bihan-Duval
- UR83 Recherches Avicoles, Institut National de la Recherche Agronomique (INRA), F-37380, Nouzilly, France
| | - M J Duclos
- UR83 Recherches Avicoles, Institut National de la Recherche Agronomique (INRA), F-37380, Nouzilly, France
| | - S E Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA, 30602, USA
| | - L A Cogburn
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.
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76
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Denzin LK, Khan AA, Virdis F, Wilks J, Kane M, Beilinson HA, Dikiy S, Case LK, Roopenian D, Witkowski M, Chervonsky AV, Golovkina TV. Neutralizing Antibody Responses to Viral Infections Are Linked to the Non-classical MHC Class II Gene H2-Ob. Immunity 2017; 47:310-322.e7. [PMID: 28813660 PMCID: PMC5568092 DOI: 10.1016/j.immuni.2017.07.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 05/23/2017] [Accepted: 07/19/2017] [Indexed: 01/08/2023]
Abstract
Select humans and animals control persistent viral infections via adaptive immune responses that include production of neutralizing antibodies. The precise genetic basis for the control remains enigmatic. Here, we report positional cloning of the gene responsible for production of retrovirus-neutralizing antibodies in mice of the I/LnJ strain. It encodes the beta subunit of the non-classical major histocompatibility complex class II (MHC-II)-like molecule H2-O, a negative regulator of antigen presentation. The recessive and functionally null I/LnJ H2-Ob allele supported the production of virus-neutralizing antibodies independently of the classical MHC haplotype. Subsequent bioinformatics and functional analyses of the human H2-Ob homolog, HLA-DOB, revealed both loss- and gain-of-function alleles, which could affect the ability of their carriers to control infections with human hepatitis B (HBV) and C (HCV) viruses. Thus, understanding of the previously unappreciated role of H2-O (HLA-DO) in immunity to infections may suggest new approaches in achieving neutralizing immunity to viruses.
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Affiliation(s)
- Lisa K Denzin
- Child Health Institute of NJ, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of NJ, New Brunswick, NJ 08901, USA
| | - Aly A Khan
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Francesca Virdis
- Child Health Institute of NJ, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of NJ, New Brunswick, NJ 08901, USA
| | - Jessica Wilks
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Melissa Kane
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Helen A Beilinson
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Stanislav Dikiy
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Laure K Case
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Michele Witkowski
- Child Health Institute of NJ, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of NJ, New Brunswick, NJ 08901, USA
| | | | - Tatyana V Golovkina
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA.
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77
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Prostaglandin dehydrogenase is a target for successful induction of cervical ripening. Proc Natl Acad Sci U S A 2017; 114:E6427-E6436. [PMID: 28716915 DOI: 10.1073/pnas.1704945114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The cervix represents a formidable structural barrier for successful induction of labor. Approximately 10% of pregnancies undergo induction of cervical ripening and labor with prostaglandin (PG) E2 or PGE analogs, often requiring many hours of hospitalization and monitoring. On the other hand, preterm cervical ripening in the second trimester predicts preterm birth. The regulatory mechanisms of this paradoxical function of the cervix are unknown. Here, we show that PGE2 uses cell-specific EP2 receptor-mediated increases in Ca2+ to dephosphorylate and translocate histone deacetylase 4 (HDAC4) to the nucleus for repression of 15-hydroxy prostaglandin dehydrogenase (15-PGDH). The crucial role of 15-PGDH in cervical ripening was confirmed in vivo. Although PGE2 or 15-PGDH inhibitor alone did not alter gestational length, treatment with 15-PGDH inhibitor + PGE2 or metabolism-resistant dimethyl-PGE2 resulted in preterm cervical ripening and delivery in mice. The ability of PGE2 to selectively autoamplify its own synthesis in stromal cells by signaling transcriptional repression of 15-PGDH elucidates long sought-after molecular mechanisms that govern PG action in the cervix. This report details unique mechanisms of action in the cervix and serves as a catalyst for (i) the use of 15-PGDH inhibitors to initiate or amplify low-dose PGE2-mediated cervical ripening or (ii) EP2 receptor antagonists, HDAC4 inhibitors, and 15-PGDH activators to prevent preterm cervical ripening and preterm birth.
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78
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Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9306564. [PMID: 28785592 PMCID: PMC5529626 DOI: 10.1155/2017/9306564] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/05/2017] [Indexed: 12/12/2022]
Abstract
Nucleic acid extraction (NAE) plays a vital role in molecular biology as the primary step for many downstream applications. Many modifications have been introduced to the original 1869 method. Modern processes are categorized into chemical or mechanical, each with peculiarities that influence their use, especially in point-of-care diagnostics (POC-Dx). POC-Dx is a new approach aiming to replace sophisticated analytical machinery with microanalytical systems, able to be used near the patient, at the point of care or point of need. Although notable efforts have been made, a simple and effective extraction method is still a major challenge for widespread use of POC-Dx. In this review, we dissected the working principle of each of the most common NAE methods, overviewing their advantages and disadvantages, as well their potential for integration in POC-Dx systems. At present, it seems difficult, if not impossible, to establish a procedure which can be universally applied to POC-Dx. We also discuss the effects of the NAE chemicals upon the main plastic polymers used to mass produce POC-Dx systems. We end our review discussing the limitations and challenges that should guide the quest for an efficient extraction method that can be integrated in a POC-Dx system.
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79
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Overexpression of CHOP in Myelinating Cells Does Not Confer a Significant Phenotype under Normal or Metabolic Stress Conditions. J Neurosci 2017; 36:6803-19. [PMID: 27335410 DOI: 10.1523/jneurosci.1118-15.2016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/23/2016] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED The PKR-like endoplasmic reticulum kinase (PERK) pathway of the unfolded protein response (UPR) is protective against toxic accumulations of misfolded proteins in the endoplasmic reticulum, but is thought to drive cell death via the transcription factor, CHOP. However, in many cell types, CHOP is an obligate step in the PERK pathway, which frames the conundrum of a prosurvival pathway that kills cells. Our laboratory and others have previously demonstrated the prosurvival activity of the PERK pathway in oligodendrocytes. In the current study, we constitutively overexpress CHOP in myelinating cells during development and into adulthood under normal or UPR conditions. We show that this transcription factor does not drive apoptosis. Indeed, we observe no detriment in mice at multiple levels from single cells to mouse behavior and life span. In light of these data and other studies, we reinterpret PERK pathway function in the context of a stochastic vulnerability model, which governs the likelihood that cells undergo cell death upon cessation of UPR protection and while attempting to restore homeostasis. SIGNIFICANCE STATEMENT Herein, we tackle the biggest controversy in the UPR literature: the function of the transcription factor CHOP as a protective or a prodeath factor. This manuscript is timely in light of the 2014 Lasker award for the UPR. Our in vivo data show that CHOP is not a prodeath protein, and we demonstrate that myelinating glial cells function normally in the presence of high CHOP expression from development to adulthood. Further, we propose a simplified view of UPR-mediated cell death after CHOP induction. We anticipate our work may turn the tide of the dogmatic view of CHOP and cause a reinvestigation of its function in different cell types. Accordingly, we believe our work will be a watershed for the UPR field.
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80
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Collagen-derived proline promotes pancreatic ductal adenocarcinoma cell survival under nutrient limited conditions. Nat Commun 2017; 8:16031. [PMID: 28685754 PMCID: PMC5504351 DOI: 10.1038/ncomms16031] [Citation(s) in RCA: 262] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/23/2017] [Indexed: 12/12/2022] Open
Abstract
Tissue architecture contributes to pancreatic ductal adenocarcinoma (PDAC) phenotypes. Cancer cells within PDAC form gland-like structures embedded in a collagen-rich meshwork where nutrients and oxygen are scarce. Altered metabolism is needed for tumour cells to survive in this environment, but the metabolic modifications that allow PDAC cells to endure these conditions are incompletely understood. Here we demonstrate that collagen serves as a proline reservoir for PDAC cells to use as a nutrient source when other fuels are limited. We show PDAC cells are able to take up collagen fragments, which can promote PDAC cell survival under nutrient limited conditions, and that collagen-derived proline contributes to PDAC cell metabolism. Finally, we show that proline oxidase (PRODH1) is required for PDAC cell proliferation in vitro and in vivo. Collectively, our results indicate that PDAC extracellular matrix represents a nutrient reservoir for tumour cells highlighting the metabolic flexibility of this cancer. Cancer cells adapt their metabolism to survive limited nutrient availability. Here, the authors show that in conditions of limited glucose or glutamine availability, pancreatic ductal adenocarcinoma cells can use collagen-derived proline to foster the TCA cycle and allow cell survival both in vitro and in vivo.
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81
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Hosomi K, Ohno H, Murakami H, Natsume-Kitatani Y, Tanisawa K, Hirata S, Suzuki H, Nagatake T, Nishino T, Mizuguchi K, Miyachi M, Kunisawa J. Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity. Sci Rep 2017; 7:4339. [PMID: 28659635 PMCID: PMC5489508 DOI: 10.1038/s41598-017-04511-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/28/2017] [Indexed: 02/07/2023] Open
Abstract
Metagenomic analysis based on the 16S rRNA gene is generally performed to examine the diversity and abundance of commensal bacteria in feces, which is now recognized to be associated with human health and diseases. Guanidine thiocyanate (GuSCN) solution is used as a less onerous way compared with a frozen method to transport and stock fecal samples at room temperature for DNA analysis; however, optimal methods to measure fecal bacterial composition in GuSCN solution remain to be investigated. Here, we examined the influence of various factors such as pretreatment (e.g., removing GuSCN solution and washing feces with phosphate-buffered saline (PBS) before mechanical lysis), fecal concentration in the GuSCN solution, storage time, and position of fecal subsampling on the 16S rRNA-based analysis of fecal bacteria in GuSCN solution. We found that pretreatment and fecal concentration affected the bacterial composition, and a little change was noted with subsampling position. Based on these results, we propose a basic protocol, including fecal sampling, sample storage, and DNA extraction, for the 16S rRNA-based analysis of bacterial composition in feces suspended in GuSCN solution.
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Affiliation(s)
- Koji Hosomi
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan
| | - Harumi Ohno
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Haruka Murakami
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Yayoi Natsume-Kitatani
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan
| | - Kumpei Tanisawa
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Soichiro Hirata
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan.,Department of Microbiology and Immunology, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan
| | - Hidehiko Suzuki
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan
| | - Takahiro Nagatake
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan
| | - Tomomi Nishino
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan
| | - Kenji Mizuguchi
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan
| | - Motohiko Miyachi
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan.
| | - Jun Kunisawa
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan. .,Department of Microbiology and Immunology, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan. .,Graduate School of Medicine, Graduate School of Pharmaceutical Sciences, Graduate School of Dentistry, Osaka University, Osaka, 565-0871, Japan. .,Division of Mucosal Immunology, Department of Microbiology and Immunology and International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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82
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Galpern WR, Frim DM, Tatter SB, Altar CA, Beal MF, Isacson O. Cell-Mediated Delivery of Brain-Derived Neurotrophic Factor Enhances Dopamine Levels in an Mpp+ Rat Model of Substantia Nigra Degeneration. Cell Transplant 2017; 5:225-32. [PMID: 8689033 DOI: 10.1177/096368979600500211] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) promotes the survival of fetal mesencephalic dopaminergic cells and protects dopaminergic neurons against the toxicity of MPP+ in vitro. Supranigral implantation of fibroblasts genetically engineered to secrete BDNF attenuates the loss of substantia nigra pars compacta (SNc) dopaminergic neurons associated with striatal infusion of MPP+ in the adult rat. Using this MPP+ rat model of nigral degeneration, we evaluated the neurochemical effects of supranigral, cell-mediated delivery of BDNF on substantia nigra (SN) dopamine (DA) content and turnover. Genetically engineered BDNF-secreting fibroblasts (~12 ng BDNF/24 h) were implanted dorsal to the SN 7 days prior to striatal MPP+ administration. The present results demonstrate that BDNF-secreting fibroblasts, as compared to control fibroblasts, enhance SN DA levels ipsilateral as well as contralateral to the graft without altering DA turnover. This augmentation of DA levels suggests that local neurotrophic factor delivery by genetically engineered cells may provide a therapeutic strategy for preventing neuronal death or enhancing neuronal function in neurodegenerative diseases characterized by dopaminergic neuronal dysfunction, such as Parkinson's disease.
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Affiliation(s)
- W R Galpern
- Neuroregeneration Laboratory, McLean Hospital, Belmont, MA 02178, USA
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83
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Macrophage Depletion Impairs Skeletal Muscle Regeneration: the Roles of Pro-fibrotic Factors, Inflammation, and Oxidative Stress. Inflammation 2017; 39:2016-2028. [PMID: 27605219 DOI: 10.1007/s10753-016-0438-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Muscle contusion is one of the most common muscle injuries in sports medicine. Macrophages play complex roles in the regeneration of skeletal muscle. However, the roles of macrophages, especially the mechanisms involved, in the regeneration of muscle contusion are still not fully understood. We hypothesize that the depletion of macrophages impairs skeletal muscle regeneration and that pro-fibrotic factors, inflammation, and oxidative stress may be involved in the process. To test these hypotheses, we constructed a muscle contusion injury and a macrophage depletion model and followed it up with morphological and gene expression analyses. The data showed that fibrotic scars were formed in the muscle of contusion injury, and they deteriorated in the mice of macrophage depletion. Furthermore, the sizes of regenerating myofibers were significantly reduced by macrophage depletion. Pro-fibrotic factors, inflammatory cytokines, chemokines, and oxidative stress-related enzymes increased significantly after muscle injury. Moreover, the expression of these factors was delayed by macrophage depletion. Most of them were still significantly higher in the later stage of regeneration. These results suggest that macrophage depletion impairs skeletal muscle regeneration and that pro-fibrotic factors, inflammation, and oxidative stress may play important roles in the process.
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84
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Yelbay B, Gow A, Jamil HM. Ranking Novel Regulatory Genes in Gene Expression Profiles using NetExpress. PROCEEDINGS OF THE ... SYMPOSIUM ON APPLIED COMPUTING. SYMPOSIUM ON APPLIED COMPUTING 2017; 2017:24-27. [PMID: 34095903 DOI: 10.1145/3019612.3021289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Understanding gene regulation by identifying gene products and determining their roles in regulatory networks is a complex process. A common computational method is to reverse engineer a regulatory network from gene expression profile, and sanitize the network using known information about the genes, their interactions and other properties to filter out unlikely interactors. Unfortunately, due to limited resources most gene expression studies have a limited and small number of time points, and most reverse engineering tools are unable to handle large numbers of genes. Both of these factors play significant roles in influencing the accuracy of the process. In this paper, we present a new gene ranking algorithm from gene expression profiles with a small number of time points so that the most relevant genes can be selected for reverse engineering. We also present a graphical interface called NetExpress, which adopts this algorithm and allows users to set control parameters to effect the desired outcome, and visualize the analysis for iterative fine tuning.
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Affiliation(s)
- Belma Yelbay
- Department of Industrial Engineering, Sabanci University, Turkey
| | - Alexander Gow
- Center for Molecular Medicine and Genetics, Wayne State University, USA
| | - Hasan M Jamil
- Department of Computer Science, University of Idaho, USA
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85
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Feng R, Li L, Li B, Li J, Peng D, Yu Y, Mu Q, Zhao N, Yu X, Wang Z. Turn-on fluorescent probes that can light up endogenous RNA in nucleoli and cytoplasm of living cells under a two-photon microscope. RSC Adv 2017. [DOI: 10.1039/c6ra28284a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We report two turn-on RNA probes that can light up endogenous RNA in the nucleoli and cytoplasm of living cells under a two-photon microscope.
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86
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Ishibashi Y, Aoki N, Kasa S, Sakamoto M, Kai K, Tomokiyo R, Watabe G, Yuasa T, Iwaya-Inoue M. The Interrelationship between Abscisic Acid and Reactive Oxygen Species Plays a Key Role in Barley Seed Dormancy and Germination. FRONTIERS IN PLANT SCIENCE 2017; 8:275. [PMID: 28377774 PMCID: PMC5359625 DOI: 10.3389/fpls.2017.00275] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/14/2017] [Indexed: 05/19/2023]
Abstract
Seed dormancy is one of the adaptive responses in the plant life cycle and an important agronomic trait. Reactive oxygen species (ROS) release seed dormancy and promote seed germination in several cereal crops; however, the key regulatory mechanism of ROS-mediated seed dormancy and germination remains controversial. Here, we focused on the relationship between hydrogen peroxide (a ROS) and abscisic acid (ABA) in dormant and non-dormant barley seeds. The hydrogen peroxide (H2O2) level produced in barley seed embryos after imbibition was higher in non-dormant seeds than in dormant seeds. H2O2 regulated the ABA content in the embryos through ABA-8'-hydroxylase, an ABA catabolic enzyme. Moreover, compared with non-dormant seeds, in dormant seeds the activity of NADPH oxidase, which produces ROS, was lower, whereas the activity of catalase, which is a H2O2 scavenging enzyme, was higher, as was the expression of HvCAT2. Furthermore, precocious germination of isolated immature embryos was suppressed by the transient introduction of HvCAT2 driven by the maize (Zea mays) ubiquitin promoter. HvCAT2 expression was regulated through an ABA-responsive transcription factor (HvABI5) induced by ABA. These results suggest that the changing of balance between ABA and ROS is active in barley seed embryos after imbibition and regulates barley seed dormancy and germination.
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87
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Abstract
In the fruit fly Drosophila melanogaster, ovarian germline stem cells (GSCs) and their niches form during larval development. This process is poorly studied partly due to technical difficulties in isolating early larval ovaries. In addition, purifying RNA from larval ovaries proves to be more challenging than purifying it from other organs. Here we describe a technique for dissecting ovaries from early larvae and advise on how to extract RNA with maximum yield and purity. RNA isolation allows assaying gene expression in a direct and quantitative manner, which is invaluable for understanding molecular events underlying ovarian niche formation and GSC establishment.
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88
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Cesen-Cummings K, Houston KD, Copland JA, Moorman VJ, Walker CL, Davis BJ. Uterine Leiomyomas Express Myometrial Contractile-Associated Proteins Involved in Pregnancy-Related Hormone Signaling. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/107155760301000104] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
| | | | | | | | - Cheryl Lyn Walker
- Laboratory of Women's Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Smithville, Texas; University of Texas Medical Branch at Galveston, Galveston, Texas
| | - Barbara J. Davis
- Laboratory of Women's Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Smithville, Texas; University of Texas Medical Branch at Galveston, Galveston, Texas; PO Box 12233, Mail Drop A2-01, Research Triangle Park, NC 27709
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89
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Zhu H, Ornaghi F, Belin S, Givogri MI, Wrabetz L, Bongarzone ER. Generation of a LacZ reporter transgenic mouse line for the stereological analysis of oligodendrocyte loss in galactosylceramidase deficiency. J Neurosci Res 2016; 94:1520-1530. [PMID: 27426866 PMCID: PMC5069144 DOI: 10.1002/jnr.23839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/10/2016] [Accepted: 06/27/2016] [Indexed: 11/11/2022]
Abstract
Krabbe's disease is a leukodystrophy resulting from deficiency of galactosylceramidase and the accumulation of galactosylsphingosine (psychosine) in the nervous system. Psychosine is believed to cause central demyelination by killing oligodendrocytes. Quantitative analysis of this process is lacking. To address this, we generated a new transgenic reporter twitcher line in which myelinating oligodendrocytes are genetically marked by the expression of LacZ under control of the myelin basic protein (MBP) promoter. MBP-LacZ-twitcher transgenic mice were used for unbiased stereological quantification of β-galactosidase+ oligodendrocytes in the spinal cord. As expected, we found decreased numbers of these cells in mutant cords, paralleling the severity of clinical disease. The decrease of oligodendrocytes does not correlate well with the increase of psychosine. The new MBP-LacZ-twitcher line will be a useful genetic tool for measuring changes in oligodendrocyte numbers in different regions of the mutant CNS and in preclinical trials of therapies to prevent demyelination. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hongling Zhu
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Francesca Ornaghi
- San Raffaele Scientific Institute, Milano, Italy
- Hunter James Kelly Research Institute, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, New York
| | - Sophie Belin
- Hunter James Kelly Research Institute, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, New York
| | - Maria I Givogri
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Lawrence Wrabetz
- Hunter James Kelly Research Institute, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, New York
| | - Ernesto R Bongarzone
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois.
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90
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Sahr A, Wolke C, Maczewsky J, Krippeit-Drews P, Tetzner A, Drews G, Venz S, Gürtler S, van den Brandt J, Berg S, Döring P, Dombrowski F, Walther T, Lendeckel U. The Angiotensin-(1-7)/Mas Axis Improves Pancreatic β-Cell Function in Vitro and in Vivo. Endocrinology 2016; 157:4677-4690. [PMID: 27715254 DOI: 10.1210/en.2016-1247] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The angiotensin-converting enzyme 2/angiotensin (Ang)-(1-7)/Mas axis of the renin-angiotensin system often opposes the detrimental effects of the angiotensin-converting enzyme/Ang II/Ang II type 1 receptor axis and has been associated with beneficial effects on glucose homeostasis, whereas underlying mechanisms are mostly unknown. Here we investigate the effects of Ang-(1-7) and its receptor Mas on β-cell function. Isolated islets from Mas-deficient and wild-type mice were stimulated with Ang-(1-7) or its antagonists and effects on insulin secretion determined. Islets' cytoplasmic calcium and cAMP concentrations, mRNA amounts of Ins1, Ins2, Pdx1, and Mafa and effects of inhibitors of cAMP downstream signaling were determined. Ang-(1-7) was also applied to mice by osmotic pumps for 14 days and effects on glucose tolerance and insulin secretion were assessed. Ang-(1-7) increased insulin secretion from wild-type islets, whereas antagonists and genetic Mas deficiency led to reduced insulin secretion. The Mas-dependent effects of Ang-(1-7) on insulin secretion did not result from changes in insulin gene expression or changes in the excitation-secretion coupling but from increased intracellular cAMP involving exchange protein activated directly by cAMP. Administration of Ang-(1-7) in vivo had only marginal effects on glucose tolerance in wild-type mice but still resulted in improved insulin secretion from islets isolated of these mice. Interestingly, although less pronounced than in wild types, Ang-(1-7) still affected insulin secretion in Mas-deficient islets. The data indicate a significant function of Ang-(1-7) in the regulation of insulin secretion from mouse islets in vitro and in vivo, mainly, but not exclusively, by Mas-dependent signaling, modulating the accessory pathway of insulin secretion via increase in cAMP.
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Affiliation(s)
- Anika Sahr
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Carmen Wolke
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Jonas Maczewsky
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Peter Krippeit-Drews
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Anja Tetzner
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Gisela Drews
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Simone Venz
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Sarah Gürtler
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Jens van den Brandt
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Sabine Berg
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Paula Döring
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Frank Dombrowski
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Thomas Walther
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Uwe Lendeckel
- Institute of Medical Biochemistry and Molecular Biology (A.S., C.W., S.V., S.G.M, U.L.), Institute of Pathology (P.D., F.D.), University Medicine Greifswald, D-17475 Greifswald, Germany; Department of Pharmacology (J.M., P.K.-D., G.D.), Institute of Pharmacy, University of Tübingen, D-72076, Tübingen, Germany; Department of Pharmacology and Therapeutics (A.T., T.W.), University College Cork, Cork, Ireland; Clinic for Pediatric Surgery and Department of Obstetrics (A.T., T.W.), University Medical Centre Leipzig, D-04103 Leipzig, Germany; and Central Core and Research Facility of Laboratory Animals (J.v.d.B., S.B.), University Medicine Greifswald, D-17489 Greifswald, Germany
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91
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Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation, and Homeostasis by PTF1A. Mol Cell Biol 2016; 36:3033-3047. [PMID: 27697859 DOI: 10.1128/mcb.00358-16] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/23/2016] [Indexed: 12/17/2022] Open
Abstract
Maintenance of cell type identity is crucial for health, yet little is known of the regulation that sustains the long-term stability of differentiated phenotypes. To investigate the roles that key transcriptional regulators play in adult differentiated cells, we examined the effects of depletion of the developmental master regulator PTF1A on the specialized phenotype of the adult pancreatic acinar cell in vivo Transcriptome sequencing and chromatin immunoprecipitation sequencing results showed that PTF1A maintains the expression of genes for all cellular processes dedicated to the production of the secretory digestive enzymes, a highly attuned surveillance of unfolded proteins, and a heightened unfolded protein response (UPR). Control by PTF1A is direct on target genes and indirect through a ten-member transcription factor network. Depletion of PTF1A causes an imbalance that overwhelms the UPR, induces cellular injury, and provokes acinar metaplasia. Compromised cellular identity occurs by derepression of characteristic stomach genes, some of which are also associated with pancreatic ductal cells. The loss of acinar cell homeostasis, differentiation, and identity is directly relevant to the pathologies of pancreatitis and pancreatic adenocarcinoma.
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92
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Wollny D, Zhao S, Everlien I, Lun X, Brunken J, Brüne D, Ziebell F, Tabansky I, Weichert W, Marciniak-Czochra A, Martin-Villalba A. Single-Cell Analysis Uncovers Clonal Acinar Cell Heterogeneity in the Adult Pancreas. Dev Cell 2016; 39:289-301. [DOI: 10.1016/j.devcel.2016.10.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/09/2023]
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93
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Mauri G, Jachetti E, Comuzzi B, Dugo M, Arioli I, Miotti S, Sangaletti S, Di Carlo E, Tripodo C, Colombo MP. Genetic deletion of osteopontin in TRAMP mice skews prostate carcinogenesis from adenocarcinoma to aggressive human-like neuroendocrine cancers. Oncotarget 2016; 7:3905-20. [PMID: 26700622 PMCID: PMC4826179 DOI: 10.18632/oncotarget.6678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 11/23/2015] [Indexed: 12/18/2022] Open
Abstract
Osteopontin (OPN) is a secreted glycoprotein, that belongs to the non-structural extracellular matrix (ECM), and its over expression in human prostate cancer has been associated with disease progression, androgen independence and metastatic ability. Nevertheless, the pathophysiology of OPN in prostate tumorigenesis has never been studied. We crossed TRansgenic Adenocarcinoma of the Mouse Prostate (TRAMP) mice with OPN deficient (OPN-/-) mice and followed tumor onset and progression in these double mutants. Ultrasound examination detected the early onset of a rapidly growing, homogeneous and spherical tumor in about 60% of OPN-/- TRAMP mice. Such neoplasms seldom occurred in parental TRAMP mice otherwise prone to adenocarcinomas and were characterized for being androgen receptor negative, highly proliferative and endowed with neuroendocrine (NE) features. Gene expression profiling showed up-regulation of genes involved in tumor progression, cell cycle and neuronal differentiation in OPN-deficient versus wild type TRAMP tumors. Down-regulated genes included key genes of TGFa pathway, including SMAD3 and Filamin, which were confirmed at the protein level. Furthermore, NE genes and particularly those characterizing early prostatic lesions of OPN-deficient mice were found to correlate with those of human prostate NE tumours. These data underscore a novel role of OPN in the early stages of prostate cancer growth, protecting against the development of aggressive NE tumors.
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Affiliation(s)
- Giorgio Mauri
- Molecular Immunology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, 20133, Milano, Italy
| | - Elena Jachetti
- Molecular Immunology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, 20133, Milano, Italy
| | - Barbara Comuzzi
- Molecular Immunology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, 20133, Milano, Italy
| | - Matteo Dugo
- Functional Genomics and Bioinformatics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, 20133, Milano, Italy
| | - Ivano Arioli
- Molecular Immunology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, 20133, Milano, Italy
| | - Silvia Miotti
- Molecular Immunology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, 20133, Milano, Italy
| | - Sabina Sangaletti
- Molecular Immunology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, 20133, Milano, Italy
| | - Emma Di Carlo
- Department of Medicine and Science of Aging, Section of Anatomic Pathology and Molecular Medicine, "G. d'Annunzio" University, 66100, Chieti, Italy.,Ce.S.I. Aging Research Center, "G. d'Annunzio" University Foundation, 66100, Chieti, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, 90127, Palermo, Italy
| | - Mario P Colombo
- Molecular Immunology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, 20133, Milano, Italy
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94
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The MET Receptor Tyrosine Kinase Confers Repair of Murine Pancreatic Acinar Cells following Acute and Chronic Injury. PLoS One 2016; 11:e0165485. [PMID: 27798657 PMCID: PMC5087859 DOI: 10.1371/journal.pone.0165485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/12/2016] [Indexed: 01/07/2023] Open
Abstract
Acinar cells represent the primary target in necroinflammatory diseases of the pancreas, including pancreatitis. The signaling pathways guiding acinar cell repair and regeneration following injury remain poorly understood. The purpose of this study was to determine the importance of Hepatocyte Growth Factor Receptor/MET signaling as an intrinsic repair mechanism for acinar cells following acute damage and chronic alcohol-associated injury. Here, we generated mice with targeted deletion of MET in adult acinar cells (MET-/-). Acute and repetitive pancreatic injury was induced in MET-/- and control mice with cerulein, and chronic injury by feeding mice Lieber-DeCarli diets containing alcohol with or without enhancement of repetitive pancreatic injury. We examined the exocrine pancreas of these mice histologically for acinar death, edema, inflammation and collagen deposition and changes in the transcriptional program. We show that MET expression is relatively low in normal adult pancreas. However, MET levels were elevated in ductal and acinar cells in human pancreatitis specimens, consistent with a role for MET in an adaptive repair mechanism. We report that genetic deletion of MET in adult murine acinar cells was linked to increased acinar cell death, chronic inflammation and delayed recovery (regeneration) of pancreatic exocrine tissue. Notably, increased pancreatic collagen deposition was detected in MET knockout mice following repetitive injury as well alcohol-associated injury. Finally, we identified specific alterations of the pancreatic transcriptome associated with MET signaling during injury, involved in tissue repair, inflammation and endoplasmic reticulum stress. Together, these data demonstrate the importance of MET signaling for acinar repair and regeneration, a novel finding that could attenuate the symptomology of pancreatic injury.
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95
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Leca J, Martinez S, Lac S, Nigri J, Secq V, Rubis M, Bressy C, Sergé A, Lavaut MN, Dusetti N, Loncle C, Roques J, Pietrasz D, Bousquet C, Garcia S, Granjeaud S, Ouaissi M, Bachet JB, Brun C, Iovanna JL, Zimmermann P, Vasseur S, Tomasini R. Cancer-associated fibroblast-derived annexin A6+ extracellular vesicles support pancreatic cancer aggressiveness. J Clin Invest 2016; 126:4140-4156. [PMID: 27701147 DOI: 10.1172/jci87734] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/29/2016] [Indexed: 12/21/2022] Open
Abstract
The intratumoral microenvironment, or stroma, is of major importance in the pathobiology of pancreatic ductal adenocarcinoma (PDA), and specific conditions in the stroma may promote increased cancer aggressiveness. We hypothesized that this heterogeneous and evolving compartment drastically influences tumor cell abilities, which in turn influences PDA aggressiveness through crosstalk that is mediated by extracellular vesicles (EVs). Here, we have analyzed the PDA proteomic stromal signature and identified a contribution of the annexin A6/LDL receptor-related protein 1/thrombospondin 1 (ANXA6/LRP1/TSP1) complex in tumor cell crosstalk. Formation of the ANXA6/LRP1/TSP1 complex was restricted to cancer-associated fibroblasts (CAFs) and required physiopathologic culture conditions that improved tumor cell survival and migration. Increased PDA aggressiveness was dependent on tumor cell-mediated uptake of CAF-derived ANXA6+ EVs carrying the ANXA6/LRP1/TSP1 complex. Depletion of ANXA6 in CAFs impaired complex formation and subsequently impaired PDA and metastasis occurrence, while injection of CAF-derived ANXA6+ EVs enhanced tumorigenesis. We found that the presence of ANXA6+ EVs in serum was restricted to PDA patients and represents a potential biomarker for PDA grade. These findings suggest that CAF-tumor cell crosstalk supported by ANXA6+ EVs is predictive of PDA aggressiveness, highlighting a therapeutic target and potential biomarker for PDA.
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96
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Palmer SS, Haynes-Johnson D, Diehl T, Nowak RA. Increased Expression of Stromelysin 3 mRNA in Leiomyomas (Uterine Fibroids) Compared With Myometrium. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/107155769800500408] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Stephen S. Palmer
- Brigham and Women's Hospital, Boston, Massachusetts; Robert Wood Johnson Pharmaceutical Research Institute, Room B-104, 1000 Route 202, PO Box 300, Raritan. NJ 08559
| | | | | | - Romana A. Nowak
- Robet Wood Johnson Pharmaceutical Research Institute, Raritan. New Jersey; Brigham and Women's Hospital, Boston, Massachusetts
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97
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Török A, Schiffer PH, Schnitzler CE, Ford K, Mullikin JC, Baxevanis AD, Bacic A, Frank U, Gornik SG. The cnidarian Hydractinia echinata employs canonical and highly adapted histones to pack its DNA. Epigenetics Chromatin 2016; 9:36. [PMID: 27602058 PMCID: PMC5011920 DOI: 10.1186/s13072-016-0085-1] [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: 06/24/2016] [Accepted: 08/24/2016] [Indexed: 11/25/2022] Open
Abstract
Background Cnidarians are a group of early branching animals including corals, jellyfish and hydroids that are renowned for their high regenerative ability, growth plasticity and longevity. Because cnidarian genomes are conventional in terms of protein-coding genes, their remarkable features are likely a consequence of epigenetic regulation. To facilitate epigenetics research in cnidarians, we analysed the histone complement of the cnidarian model organism Hydractinia echinata using phylogenomics, proteomics, transcriptomics and mRNA in situ hybridisations. Results We find that the Hydractinia genome encodes 19 histones and analyse their spatial expression patterns, genomic loci and replication-dependency. Alongside core and other replication-independent histone variants, we find several histone replication-dependent variants, including a rare replication-dependent H3.3, a female germ cell-specific H2A.X and an unusual set of five H2B variants, four of which are male germ cell-specific. We further confirm the absence of protamines in Hydractinia. Conclusions Since no protamines are found in hydroids, we suggest that the novel H2B variants are pivotal for sperm DNA packaging in this class of Cnidaria. This study adds to the limited number of full histone gene complements available in animals and sets a comprehensive framework for future studies on the role of histones and their post-translational modifications in cnidarian epigenetics. Finally, it provides insight into the evolution of spermatogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0085-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Török
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Philipp H Schiffer
- Genetics Environment and Evolution, University College London, London, UK
| | - Christine E Schnitzler
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ; Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA
| | - Kris Ford
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA ; Australian Research Council Centre of Excellence in Plant Cell Walls, School of Biosciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - James C Mullikin
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20852 USA
| | - Andreas D Baxevanis
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Biosciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Uri Frank
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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98
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Hurwitz A, Ruutiainen-Altman K, Marzella L, Botero L, Dushnik M, Adashi EY. Follicular Atresia as an Apoptotic Process: Atresia-Associated Increase in the Ovarian Expression of the Putative Apoptotic Marker Sulfated Glycoprotein-2. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/107155769600300407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | | | - Louis Marzella
- Division os Reproductive Endocrinology, Department of Obstetnes and Gynecology, and the Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Luis Botero
- Division os Reproductive Endocrinology, Department of Obstetnes and Gynecology, and the Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland; Universidad Javeriana, Hospital San Ignacio, Departamento de Gineco-Obstetricia (3rd PISO), Bogota, Colombia
| | - Matat Dushnik
- Division os Reproductive Endocrinology, Department of Obstetnes and Gynecology, and the Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Eli Y. Adashi
- Division os Reproductive Endocrinology, Department of Obstetnes and Gynecology, and the Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland; Division of Reproductive Endocrinology, Departments of Obstetrics/Gynecology and Physiology, 405 W. Redwood Street, Third Floor, Baltimore, MD 21201
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99
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Hirst JJ, Mijovic JE, Zakar T, Olson DM. Prostaglandin Endoperoxide H Synthase-1 and -2 mRNA Levels and Enzyme Activity in Human Decidua at Term Labor. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/107155769800500104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jonathan J. Hirst
- Perinatal Research Centre, Departments of Obstetrics and Gynaecology and Pediatrics and Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Jane E. Mijovic
- Perinatal Research Centre, Departments of Obstetrics and Gynaecology and Pediatrics and Physiology, University of Alberta, Edmonton, Alberta, Canada; Perinatal Research Centre, Room 220 Heritage Medical Research Building, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | | | - David M. Olson
- Perinatal Research Centre, Departments of Obstetrics and Gynaecology and Pediatrics and Physiology, University of Alberta, Edmonton, Alberta, Canada
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100
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Rehman KS, Carr BR, Rainey WE. Profiling the Steroidogenic Pathway in Human Fetal and Adult Adrenals. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/s1071-55760300118-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
| | - Bruce R. Carr
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - William E. Rainey
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9032
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