47551
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Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nat Ecol Evol 2016; 1:14. [PMID: 28812568 DOI: 10.1038/s41559-016-0014] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/07/2016] [Indexed: 02/07/2023]
Abstract
Local adaptation is ubiquitous, but the molecular mechanisms that give rise to this ecological phenomenon remain largely unknown. A year-long reciprocal transplant of mustard hill coral (Porites astreoides) between a highly environmentally variable inshore habitat and a more stable offshore habitat demonstrated that populations exhibit phenotypic signatures that are consistent with local adaptation. We characterized the genomic basis of this adaptation in both coral hosts and their intracellular symbionts (Symbiodinium sp.) using genome-wide gene expression profiling. Populations differed primarily in their capacity for plasticity: following transplantation to a novel environment, inshore-origin coral expression profiles became significantly more similar to the local population's profiles than those in offshore-origin corals. Furthermore, elevated plasticity of the environmental stress response expression was correlated with lower susceptibility to a natural summer bleaching event, suggesting that plasticity is adaptive in the inshore environment. Our results reveal a novel genomic mechanism of resilience to a variable environment, demonstrating that corals are capable of a more diverse molecular response to stress than previously thought.
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47552
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Iwai S, Weinmaier T, Schmidt BL, Albertson DG, Poloso NJ, Dabbagh K, DeSantis TZ. Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes. PLoS One 2016; 11:e0166104. [PMID: 27820856 PMCID: PMC5098786 DOI: 10.1371/journal.pone.0166104] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/07/2016] [Indexed: 01/30/2023] Open
Abstract
Functional analysis of a clinical microbiome facilitates the elucidation of mechanisms by which microbiome perturbation can cause a phenotypic change in the patient. The direct approach for the analysis of the functional capacity of the microbiome is via shotgun metagenomics. An inexpensive method to estimate the functional capacity of a microbial community is through collecting 16S rRNA gene profiles then indirectly inferring the abundance of functional genes. This inference approach has been implemented in the PICRUSt and Tax4Fun software tools. However, those tools have important limitations since they rely on outdated functional databases and uncertain phylogenetic trees and require very specific data pre-processing protocols. Here we introduce Piphillin, a straightforward algorithm independent of any proposed phylogenetic tree, leveraging contemporary functional databases and not obliged to any singular data pre-processing protocol. When all three inference tools were evaluated against actual shotgun metagenomics, Piphillin was superior in predicting gene composition in human clinical samples compared to both PICRUSt and Tax4Fun (p<0.01 and p<0.001, respectively) and Piphillin’s ability to predict disease associations with specific gene orthologs exhibited a 15% increase in balanced accuracy compared to PICRUSt. From laboratory animal samples, no performance advantage was observed for any one of the tools over the others and for environmental samples all produced unsatisfactory predictions. Our results demonstrate that functional inference using the direct method implemented in Piphillin is preferable for clinical biospecimens. Piphillin is publicly available for academic use at http://secondgenome.com/Piphillin.
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Affiliation(s)
- Shoko Iwai
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
| | - Thomas Weinmaier
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
| | - Brian L. Schmidt
- Bluestone Center for Clinical Research and the Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, New York, United States of America
| | - Donna G. Albertson
- Bluestone Center for Clinical Research and the Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, New York, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Neil J. Poloso
- Research and External Scientific Innovation Department, Allergan PLC, Irvine, California, United States of America
| | - Karim Dabbagh
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
| | - Todd Z. DeSantis
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
- * E-mail:
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47553
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Bain PA, Gregg AL, Kumar A. De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water. BMC Genomics 2016; 17:890. [PMID: 27821072 PMCID: PMC5100079 DOI: 10.1186/s12864-016-3208-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/25/2016] [Indexed: 12/29/2022] Open
Abstract
Background The atyid shrimp Paratya australiensis occurs in surface freshwater habitats throughout eastern Australia and has been used to study the ecotoxicology of contaminants such as pesticides and metals. The acidification of surface water that can occur after acid sulfate material in soils and sediments is oxidised and subsequently re-wetted is a serious environmental issue in coastal regions and inland riverine floodplains worldwide. Solubilisation of soil-associated minerals can result in high waterborne concentrations of mineral salts and dissolved metals, which together with low pH represent a potential threat to aquatic ecosystems in affected regions. The aims of the present study were to gain insight into stress responses induced by exposure to acid drainage water (ADW) in P. australiensis by determining changes in the abundance of protein-coding transcripts and to generate a comprehensive transcriptomic resource to facilitate further research into gene regulation or protein structure and function in this species. Adult P. australiensis were exposed for 24 h to undiluted ADW, 50 % ADW diluted in river water, or to river water as control, and high-throughput mRNA sequencing (RNA-Seq) conducted on whole-body tissues. A reference transcriptome was generated using de novo assembly and putative protein-coding regions were identified and annotated. Changes in transcript abundance in response to ADW exposure were determined by aligning reads to the reference transcriptome and quantifying coverage. Results A high proportion of arthropod benchmarking universal single-copy orthologues were present in the reference transcriptome. Functions associated with cuticle biosynthesis and oxidative stress were significantly enriched in the lists of transcripts exhibiting differential abundance in either direction after exposure to 50 % or 100 % ADW. Transcripts involved in osmoregulation exhibited decreased abundance following exposure to ADW. The transcriptome contained full-length coding sequences for numerous proteins known to be involved in environmental response pathways, including two putative metallothioneins, four glutathione peroxidases and 19 nuclear receptors. Conclusions The results of the present study provide insight into stress response pathways induced in crustaceans by short-term exposure to multiple stressors present in ADW such as low pH, high salinity and dissolved metals, and represent a resource for future toxicogenomics and protein functional studies in P. australiensis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3208-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter A Bain
- Commonwealth Scientific and Industrial Research Organisation, Waite Road, Urrbrae, 5064, Australia. .,Commonwealth Scientific and Industrial Research Organisation, Private Mail Bag 2, Glen Osmond, 5064, Australia.
| | - Adrienne L Gregg
- Commonwealth Scientific and Industrial Research Organisation, Waite Road, Urrbrae, 5064, Australia
| | - Anupama Kumar
- Commonwealth Scientific and Industrial Research Organisation, Waite Road, Urrbrae, 5064, Australia
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47554
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Vasli N, Harris E, Karamchandani J, Bareke E, Majewski J, Romero NB, Stojkovic T, Barresi R, Tasfaout H, Charlton R, Malfatti E, Bohm J, Marini-Bettolo C, Choquet K, Dicaire MJ, Shao YH, Topf A, O'Ferrall E, Eymard B, Straub V, Blanco G, Lochmüller H, Brais B, Laporte J, Tétreault M. Recessive mutations in the kinase ZAK cause a congenital myopathy with fibre type disproportion. Brain 2016; 140:37-48. [PMID: 27816943 DOI: 10.1093/brain/aww257] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/03/2016] [Accepted: 08/31/2016] [Indexed: 01/09/2023] Open
Abstract
Congenital myopathies define a heterogeneous group of neuromuscular diseases with neonatal or childhood hypotonia and muscle weakness. The genetic cause is still unknown in many patients, precluding genetic counselling and better understanding of the physiopathology. To identify novel genetic causes of congenital myopathies, exome sequencing was performed in three consanguineous families. We identified two homozygous frameshift mutations and a homozygous nonsense mutation in the mitogen-activated protein triple kinase ZAK. In total, six affected patients carry these mutations. Reverse transcription polymerase chain reaction and transcriptome analyses suggested nonsense mRNA decay as a main impact of mutations. The patients demonstrated a generalized slowly progressive muscle weakness accompanied by decreased vital capacities. A combination of proximal contractures with distal joint hyperlaxity is a distinct feature in one family. The low endurance and compound muscle action potential amplitude were strongly ameliorated on treatment with anticholinesterase inhibitor in another patient. Common histopathological features encompassed fibre size variation, predominance of type 1 fibre and centralized nuclei. A peculiar subsarcolemmal accumulation of mitochondria pointing towards the centre of the fibre was a novel histological hallmark in one family. These findings will improve the molecular diagnosis of congenital myopathies and implicate the mitogen-activated protein kinase (MAPK) signalling as a novel pathway altered in these rare myopathies.
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Affiliation(s)
- Nasim Vasli
- 1 Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1, rue Laurent Fries, BP 10142, 67404 Illkirch, France.,2 INSERM U974, 67404 Illkirch, France.,3 CNRS, UMR7104, 67404 Illkirch, France.,4 Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67404 Illkirch, France
| | - Elizabeth Harris
- 5 John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Jason Karamchandani
- 6 Department of Pathology, McGill University Health Centre, Montreal Neurological Institute Hospital, Montreal, QC H3A 2B4, Canada
| | - Eric Bareke
- 7 Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada.,8 McGill University and Genome Quebec Innovation Center, Montreal, QC H3A 1A4, Canada
| | - Jacek Majewski
- 7 Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada.,8 McGill University and Genome Quebec Innovation Center, Montreal, QC H3A 1A4, Canada
| | - Norma B Romero
- 9 Université Sorbonne, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, GH Pitié-Salpêtrière, 47 Boulevard de l'hôpital, 75013 Paris, France.,10 Centre de référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Tanya Stojkovic
- 10 Centre de référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Rita Barresi
- 5 John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Hichem Tasfaout
- 1 Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1, rue Laurent Fries, BP 10142, 67404 Illkirch, France.,2 INSERM U974, 67404 Illkirch, France.,3 CNRS, UMR7104, 67404 Illkirch, France.,4 Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67404 Illkirch, France
| | - Richard Charlton
- 5 John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Edoardo Malfatti
- 9 Université Sorbonne, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, GH Pitié-Salpêtrière, 47 Boulevard de l'hôpital, 75013 Paris, France.,10 Centre de référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Johann Bohm
- 1 Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1, rue Laurent Fries, BP 10142, 67404 Illkirch, France.,2 INSERM U974, 67404 Illkirch, France.,3 CNRS, UMR7104, 67404 Illkirch, France.,4 Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67404 Illkirch, France
| | - Chiara Marini-Bettolo
- 5 John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Karine Choquet
- 7 Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada.,11 Rare Neurological Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Marie-Josée Dicaire
- 11 Rare Neurological Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Yi-Hong Shao
- 11 Rare Neurological Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Ana Topf
- 5 John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Erin O'Ferrall
- 6 Department of Pathology, McGill University Health Centre, Montreal Neurological Institute Hospital, Montreal, QC H3A 2B4, Canada
| | - Bruno Eymard
- 10 Centre de référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Volker Straub
- 5 John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Gonzalo Blanco
- 12 Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Hanns Lochmüller
- 5 John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Bernard Brais
- 7 Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada.,11 Rare Neurological Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jocelyn Laporte
- 1 Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1, rue Laurent Fries, BP 10142, 67404 Illkirch, France .,2 INSERM U974, 67404 Illkirch, France.,3 CNRS, UMR7104, 67404 Illkirch, France.,4 Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67404 Illkirch, France
| | - Martine Tétreault
- 7 Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada .,8 McGill University and Genome Quebec Innovation Center, Montreal, QC H3A 1A4, Canada
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47555
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Gim J, Won S, Park T. Conditional estimation of local pooled dispersion parameter in small-sample RNA-Seq data improves differential expression test. J Bioinform Comput Biol 2016; 14:1644006. [PMID: 27774873 DOI: 10.1142/s0219720016440066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High throughput sequencing technology in transcriptomics studies contribute to the understanding of gene regulation mechanism and its cellular function, but also increases a need for accurate statistical methods to assess quantitative differences between experiments. Many methods have been developed to account for the specifics of count data: non-normality, a dependence of the variance on the mean, and small sample size. Among them, the small number of samples in typical experiments is still a challenge. Here we present a method for differential analysis of count data, using conditional estimation of local pooled dispersion parameters. A comprehensive evaluation of our proposed method in the aspect of differential gene expression analysis using both simulated and real data sets shows that the proposed method is more powerful than other existing methods while controlling the false discovery rates. By introducing conditional estimation of local pooled dispersion parameters, we successfully overcome the limitation of small power and enable a powerful quantitative analysis focused on differential expression test with the small number of samples.
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Affiliation(s)
- Jungsoo Gim
- * Institute of Health and Environment, Seoul National University, Gwanak-gu Seoul, 151-747, South Korea
| | - Sungho Won
- † Graduate School of Public Health, Seoul National University, Gwanak-gu Seoul, 151-747, South Korea
| | - Taesung Park
- ‡ Department of Statistics, Seoul National University, Gwanak-gu Seoul, 151-747, South Korea
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47556
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Frerichs A, Thoma R, Abdallah AT, Frommolt P, Werr W, Chandler JW. The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem. BMC Genomics 2016; 17:855. [PMID: 27809788 PMCID: PMC5093967 DOI: 10.1186/s12864-016-3189-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 10/22/2016] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem flanks where they differentiate, remains largely unknown. We have combined fluorescence-activated cell sorting and RNA-seq to characterise the cell-type-specific transcriptome at the earliest developmental time-point of lateral organ formation using DORNRÖSCHEN-LIKE::GFP to mark founder-cell populations at the periphery of the inflorescence meristem (IM) in apetala1 cauliflower double mutants, which overproliferate IMs. RESULTS Within the lateral organ founder-cell population at the inflorescence meristem, floral primordium identity genes are upregulated and stem-cell identity markers are downregulated. Additional differentially expressed transcripts are involved in polarity generation and boundary formation, and in epigenetic and post-translational changes. However, only subtle transcriptional reprogramming within the global auxin network was observed. CONCLUSIONS The transcriptional network of differentially expressed genes supports the hypothesis that lateral organ founder-cell specification involves the creation of polarity from the centre to the periphery of the IM and the establishment of a boundary from surrounding cells, consistent with bract initiation. However, contrary to the established paradigm that sites of auxin response maxima pre-pattern lateral organ initiation in the IM, auxin response might play a minor role in the earliest stages of lateral floral initiation.
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Affiliation(s)
- Anneke Frerichs
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, D-50674, Cologne, Germany
| | - Rahere Thoma
- Present address: Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829, Cologne, Germany
| | - Ali Taleb Abdallah
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Peter Frommolt
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Wolfgang Werr
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, D-50674, Cologne, Germany
| | - John William Chandler
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, D-50674, Cologne, Germany.
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47557
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Clevenger J, Marasigan K, Liakos V, Sobolev V, Vellidis G, Holbrook C, Ozias-Akins P. RNA Sequencing of Contaminated Seeds Reveals the State of the Seed Permissive for Pre-Harvest Aflatoxin Contamination and Points to a Potential Susceptibility Factor. Toxins (Basel) 2016; 8:E317. [PMID: 27827875 PMCID: PMC5127114 DOI: 10.3390/toxins8110317] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/26/2016] [Accepted: 10/28/2016] [Indexed: 11/24/2022] Open
Abstract
Pre-harvest aflatoxin contamination (PAC) is a major problem facing peanut production worldwide. Produced by the ubiquitous soil fungus, Aspergillus flavus, aflatoxin is the most naturally occurring known carcinogen. The interaction between fungus and host resulting in PAC is complex, and breeding for PAC resistance has been slow. It has been shown that aflatoxin production can be induced by applying drought stress as peanut seeds mature. We have implemented an automated rainout shelter that controls temperature and moisture in the root and peg zone to induce aflatoxin production. Using polymerase chain reaction (PCR) and high performance liquid chromatography (HPLC), seeds meeting the following conditions were selected: infected with Aspergillus flavus and contaminated with aflatoxin; and not contaminated with aflatoxin. RNA sequencing analysis revealed groups of genes that describe the transcriptional state of contaminated vs. uncontaminated seed. These data suggest that fatty acid biosynthesis and abscisic acid (ABA) signaling are altered in contaminated seeds and point to a potential susceptibility factor, ABR1, as a repressor of ABA signaling that may play a role in permitting PAC.
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Affiliation(s)
- Josh Clevenger
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Tifton, GA 31793, USA.
| | - Kathleen Marasigan
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Tifton, GA 31793, USA.
| | - Vasileios Liakos
- Department of Crop and Soil Sciences, The University of Georgia, Tifton, GA 31793, USA.
| | - Victor Sobolev
- USDA-ARS National Peanut Research Laboratory, Dawson, GA 39842, USA.
| | - George Vellidis
- Department of Crop and Soil Sciences, The University of Georgia, Tifton, GA 31793, USA.
| | - Corley Holbrook
- USDA-ARS, Crop Genetics and Breeding Res. Unit, Tifton, GA 31793, USA.
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Tifton, GA 31793, USA.
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47558
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Berger M, Puinean AM, Randall E, Zimmer CT, Silva WM, Bielza P, Field LM, Hughes D, Mellor I, Hassani-Pak K, Siqueira HAA, Williamson MS, Bass C. Insecticide resistance mediated by an exon skipping event. Mol Ecol 2016; 25:5692-5704. [PMID: 27748560 PMCID: PMC5111602 DOI: 10.1111/mec.13882] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/05/2016] [Accepted: 10/05/2016] [Indexed: 12/31/2022]
Abstract
Many genes increase coding capacity by alternate exon usage. The gene encoding the insect nicotinic acetylcholine receptor (nAChR) α6 subunit, target of the bio‐insecticide spinosad, is one example of this and expands protein diversity via alternative splicing of mutually exclusive exons. Here, we show that spinosad resistance in the tomato leaf miner, Tuta absoluta is associated with aberrant regulation of splicing of Taα6 resulting in a novel form of insecticide resistance mediated by exon skipping. Sequencing of the α6 subunit cDNA from spinosad selected and unselected strains of T. absoluta revealed all Taα6 transcripts of the selected strain were devoid of exon 3, with comparison of genomic DNA and mRNA revealing this is a result of exon skipping. Exon skipping cosegregated with spinosad resistance in survival bioassays, and functional characterization of this alteration using modified human nAChR α7, a model of insect α6, demonstrated that exon 3 is essential for receptor function and hence spinosad sensitivity. DNA and RNA sequencing analyses suggested that exon skipping did not result from genetic alterations in intronic or exonic cis‐regulatory elements, but rather was associated with a single epigenetic modification downstream of exon 3a, and quantitative changes in the expression of trans‐acting proteins that have known roles in the regulation of alternative splicing. Our results demonstrate that the intrinsic capacity of the α6 gene to generate transcript diversity via alternative splicing can be readily exploited during the evolution of resistance and identifies exon skipping as a molecular alteration conferring insecticide resistance.
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Affiliation(s)
- Madeleine Berger
- Rothamsted Research, Harpenden, AL5 2JQ, UK.,School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | | | - Emma Randall
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - Christoph T Zimmer
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - Wellington M Silva
- Departamento de Agronomia-(Entomologia), Universidade Federal Rural de Pernambuco, 52171-900, Recife, PE, Brazil
| | - Pablo Bielza
- Departamento de Producción Vegetal, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, Cartagena, 30203, Spain
| | | | | | - Ian Mellor
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | | | - Herbert A A Siqueira
- Departamento de Agronomia-(Entomologia), Universidade Federal Rural de Pernambuco, 52171-900, Recife, PE, Brazil
| | | | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
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47559
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Polinski MP, Bradshaw JC, Inkpen SM, Richard J, Fritsvold C, Poppe TT, Rise ML, Garver KA, Johnson SC. De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection. BMC Genomics 2016; 17:848. [PMID: 27806699 PMCID: PMC5094019 DOI: 10.1186/s12864-016-3196-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 10/22/2016] [Indexed: 12/19/2022] Open
Abstract
Background Piscine reovirus (PRV) has been associated with the serious disease known as Heart and Skeletal Muscle Inflammation (HSMI) in cultured Atlantic salmon Salmo salar in Norway. PRV is also prevalent in wild and farmed salmon without overt disease manifestations, suggesting multifactorial triggers or PRV variant-specific factors are required to initiate disease. In this study, we explore the head kidney transcriptome of Sockeye salmon Oncorhynchus nerka during early PRV infection to identify host responses in the absence of disease in hopes of elucidating mechanisms by which PRV may directly alter host functions and contribute to the development of a disease state. We further investigate the role of PRV as a coinfecting agent following superinfection with infectious hematopoietic necrosis virus (IHNV) – a highly pathogenic rhabdovirus endemic to the west coast of North America. Results Challenge of Sockeye salmon with PRV resulted in high quantities of viral transcripts to become present in the blood and kidney of infected fish without manifestations of disease. De novo transcriptome assembly of over 2.3 billion paired RNA-seq reads from the head kidneys of 36 fish identified more than 320,000 putative unigenes, of which less than 20 were suggested to be differentially expressed in response to PRV at either 2 or 3 weeks post challenge by DESeq2 and edgeR analysis. Of these, only one, Ependymin, was confirmed to be differentially expressed by qPCR in an expanded sample set. In contrast, IHNV induced substantial transcriptional changes (differential expression of > 20,000 unigenes) which included transcripts involved in antiviral and inflammatory response pathways. Prior infection with PRV had no significant effect on host responses to superinfecting IHNV, nor did host responses initiated by IHNV exposure influence increasing PRV loads. Conclusions PRV does not substantially alter the head kidney transcriptome of Sockeye salmon during early (2 to 3 week) infection and dissemination in a period of significant increasing viral load, nor does the presence of PRV change the host transcriptional response to an IHNV superinfection. Further, concurrent infections of PRV and IHNV do not appear to significantly influence the infectivity or severity of IHNV associated disease, or conversely, PRV load. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3196-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark P Polinski
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC, V9T6N7, Canada.
| | - Julia C Bradshaw
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC, V9T6N7, Canada
| | - Sabrina M Inkpen
- Department of Ocean Sciences, Memorial University, St. John's, NF, A1C5S7, Canada
| | - Jon Richard
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC, V9T6N7, Canada
| | - Camilla Fritsvold
- Department of Pathology, Norwegian Veterinary Institute, Oslo, NO-0106, Norway
| | - Trygve T Poppe
- Department of Pathology, Norwegian Veterinary Institute, Oslo, NO-0106, Norway.,Department of Basic Sciences and Aquatic Medicine (Basam), Norwegian University of Life Sciences, P.O. Box 8146, Dep, N-0033, Oslo, Norway
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University, St. John's, NF, A1C5S7, Canada
| | - Kyle A Garver
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC, V9T6N7, Canada
| | - Stewart C Johnson
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC, V9T6N7, Canada
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47560
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Stokowy T, Wojtas B, Jarzab B, Krohn K, Fredman D, Dralle H, Musholt T, Hauptmann S, Lange D, Hegedüs L, Paschke R, Eszlinger M. Two-miRNA classifiers differentiate mutation-negative follicular thyroid carcinomas and follicular thyroid adenomas in fine needle aspirations with high specificity. Endocrine 2016; 54:440-447. [PMID: 27473101 DOI: 10.1007/s12020-016-1021-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/13/2016] [Indexed: 12/16/2022]
Abstract
Diagnosis of thyroid by fine needle aspiration is challenging for the "indeterminate" category and can be supported by molecular testing. We set out to identify miRNA markers that could be used in a diagnostic setting to improve the discrimination of mutation-negative indeterminate fine needle aspirations. miRNA high-throughput sequencing was performed for freshly frozen tissue samples of 19 RAS and PAX8/PPARG mutation-negative follicular thyroid carcinomas, and 23 RAS and PAX8/PPARG mutation-negative follicular adenomas. Differentially expressed miRNAs were validated by quantitative polymerase chain reaction in a set of 44 fine needle aspiration samples representing 24 follicular thyroid carcinomas and 20 follicular adenomas. Twenty-six miRNAs characterized by a significant differential expression between follicular thyroid carcinomas and follicular adenomas were identified. Nevertheless, since no single miRNA had satisfactory predictive power, classifiers comprising two differentially expressed miRNAs were designed with the aim to improve the classification. Six two-miRNA classifiers were established and quantitative polymerase chain reaction validated in fine needle aspiration samples. Four out of six classifiers were characterized by a high specificity (≥94 %). The best two-miRNA classifier (miR-484/miR-148b-3p) identified thyroid malignancy with a sensitivity of 89 % and a specificity of 87 %. The high-throughput sequencing allowed the identification of subtle differences in the miRNA expression profiles of follicular thyroid carcinomas and follicular adenomas. While none of the differentially expressed miRNAs could be used as a stand-alone malignancy marker, the validation results for two-miRNA classifiers in an independent set of fine needle aspirations are very promising. The ultimate evaluation of these classifiers for their capability of discriminating mutation-negative indeterminate fine needle aspirations will require the evaluation of a sufficiently large number of fine needle aspirations with histological confirmation.
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Affiliation(s)
- Tomasz Stokowy
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Nuclear Medicine and Endocrine Oncology, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, and Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Bartosz Wojtas
- Department of Nuclear Medicine and Endocrine Oncology, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, and Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Barbara Jarzab
- Department of Nuclear Medicine and Endocrine Oncology, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, and Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Knut Krohn
- IZKF Leipzig, University of Leipzig, Leipzig, Germany
| | - David Fredman
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Henning Dralle
- Department of General, Visceral and Vascular Surgery, University of Halle-Wittenberg, Halle (Saale), Germany
| | - Thomas Musholt
- Department of General, Visceral, and Transplantation Surgery, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Steffen Hauptmann
- Department of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Dariusz Lange
- Tumor Pathology Department, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
| | - László Hegedüs
- Department of Endocrinology and Metabolism, Odense University Hospital, Odense, Denmark
| | - Ralf Paschke
- Division of Endocrinology and Metabolism, Departments of Medicine and Oncology and Arnie Charbonneau Cancer Institute, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Markus Eszlinger
- Department of Oncology and Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Divisions of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany.
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47561
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Gonzalez R, Garitaonandia I, Poustovoitov M, Abramihina T, McEntire C, Culp B, Attwood J, Noskov A, Christiansen-Weber T, Khater M, Mora-Castilla S, To C, Crain A, Sherman G, Semechkin A, Laurent LC, Elsworth JD, Sladek J, Snyder EY, Redmond DE, Kern RA. Neural Stem Cells Derived from Human Parthenogenetic Stem Cells Engraft and Promote Recovery in a Nonhuman Primate Model of Parkinson's Disease. Cell Transplant 2016; 25:1945-1966. [DOI: 10.3727/096368916x691682] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cell therapy has attracted considerable interest as a promising therapeutic alternative for patients with Parkinson's disease (PD). Clinical studies have shown that grafted fetal neural tissue can achieve considerable biochemical and clinical improvements in PD. However, the source of fetal tissue grafts is limited and ethically controversial. Human parthenogenetic stem cells offer a good alternative because they are derived from unfertilized oocytes without destroying potentially viable human embryos and can be used to generate an unlimited supply of neural cells for transplantation. We have previously reported that human parthenogenetic stem cell-derived neural stem cells (hpNSCs) successfully engraft, survive long term, and increase brain dopamine (DA) levels in rodent and nonhuman primate models of PD. Here we report the results of a 12-month transplantation study of hpNSCs in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-lesioned African green monkeys with moderate to severe clinical parkinsonian symptoms. The hpNSCs manufactured under current good manufacturing practice (cGMP) conditions were injected bilaterally into the striatum and substantia nigra of immunosuppressed monkeys. Transplantation of hpNSCs was safe and well tolerated by the animals with no dyskinesia, tumors, ectopic tissue formation, or other test article-related serious adverse events. We observed that hpNSCs promoted behavioral recovery; increased striatal DA concentration, fiber innervation, and number of dopaminergic neurons; and induced the expression of genes and pathways downregulated in PD compared to vehicle control animals. These results provide further evidence for the clinical translation of hpNSCs and support the approval of the world's first pluripotent stem cell-based phase I/IIa study for the treatment of PD (Clinical Trial Identifier NCT02452723).
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Affiliation(s)
| | | | | | | | | | - Ben Culp
- Axion Research Foundation, Hamden, CT, USA
| | | | | | | | - Marwa Khater
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sergio Mora-Castilla
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cuong To
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrew Crain
- Stem Cell Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Glenn Sherman
- International Stem Cell Corporation, Carlsbad, CA, USA
| | | | - Louise C. Laurent
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - John D. Elsworth
- Department of Psychiatry and Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - John Sladek
- Department of Neurology, Pediatrics and Neuroscience, University of Colorado School of Medicine, Aurora, CO, USA
| | - Evan Y. Snyder
- Stem Cell Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - D. Eugene Redmond
- Axion Research Foundation, Hamden, CT, USA
- Department of Psychiatry and Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
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47562
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Raper J, Bosinger S, Johnson Z, Tharp G, Moran SP, Chan AWS. Increased irritability, anxiety, and immune reactivity in transgenic Huntington's disease monkeys. Brain Behav Immun 2016; 58:181-190. [PMID: 27395434 PMCID: PMC5067193 DOI: 10.1016/j.bbi.2016.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 12/20/2022] Open
Abstract
Although the most notable clinical symptoms of Huntington's disease (HD) are motor disturbances and brain atrophy, other symptoms include cognitive dysfunction, emotional and hormonal dysregulation. Emotional dysregulation (irritability, anger/aggression, and anxiety) and increased inflammation are early emerging symptoms which can be detected decades before the onset of motor symptoms in HD patients. Despite the advances in understanding the genetic causes of HD there is still no cure or preventative treatment. Thus, to better understand the pathogenesis of HD and develop effective treatments, a holistic understanding of HD is needed, as well as animal models that replicate the full spectrum of HD symptoms. The current study examined the emotional, hormonal, and gene expression responses to an acute stressor of adult male transgenic HD rhesus monkeys (n=2) as compared to wild-type controls (n=2). Results revealed that HD monkeys expressed increased anxiety and irritability/aggression as compared to controls. Reactive cortisol response to the stressor was similar between groups. However, HD monkeys exhibited increased pro-inflammatory cytokines and higher induction of immune pathway genes as compared to controls. Overall, results reveal that HD monkeys exhibit these early emerging symptoms of HD and may be an effective animal model to facilitate the development of new therapeutics for HD patients.
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Affiliation(s)
- Jessica Raper
- Yerkes National Primate Research Center, 954 Gatewood Rd NE, Atlanta, GA 30329, USA; Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA 30322, USA.
| | - Steven Bosinger
- Yerkes National Primate Research Center, 954 Gatewood Rd NE, Atlanta, GA 30329, USA.
| | - Zachary Johnson
- Yerkes National Primate Research Center, 954 Gatewood Rd NE, Atlanta, GA 30329, USA.
| | - Gregory Tharp
- Yerkes National Primate Research Center, 954 Gatewood Rd NE, Atlanta, GA 30329, USA.
| | - Sean P Moran
- Yerkes National Primate Research Center, 954 Gatewood Rd NE, Atlanta, GA 30329, USA.
| | - Anthony W S Chan
- Yerkes National Primate Research Center, 954 Gatewood Rd NE, Atlanta, GA 30329, USA; Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA 30322, USA.
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47563
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Chinen T, Kannan AK, Levine AG, Fan X, Klein U, Zheng Y, Gasteiger G, Feng Y, Fontenot JD, Rudensky AY. An essential role for the IL-2 receptor in T reg cell function. Nat Immunol 2016; 17:1322-1333. [PMID: 27595233 PMCID: PMC5071159 DOI: 10.1038/ni.3540] [Citation(s) in RCA: 571] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/27/2016] [Indexed: 12/12/2022]
Abstract
Regulatory T cells (Treg cells), which have abundant expression of the interleukin 2 receptor (IL-2R), are reliant on IL-2 produced by activated T cells. This feature indicates a key role for a simple network based on the consumption of IL-2 by Treg cells in their suppressor function. However, congenital deficiency in IL-2R results in reduced expression of the Treg cell lineage-specification factor Foxp3, which has confounded experimental efforts to understand the role of IL-2R expression and signaling in the suppressor function of Treg cells. Using genetic gain- and loss-of-function approaches, we found that capture of IL-2 was dispensable for the control of CD4+ T cells but was important for limiting the activation of CD8+ T cells, and that IL-2R-dependent activation of the transcription factor STAT5 had an essential role in the suppressor function of Treg cells separable from signaling via the T cell antigen receptor.
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Affiliation(s)
- Takatoshi Chinen
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Andrew G Levine
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiying Fan
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ulf Klein
- Herbert Irving Comprehensive Cancer Center, Department of Pathology and Cell Biology, and Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Ye Zheng
- Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Georg Gasteiger
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute for Medical Microbiology and Hygiene, University of Mainz Medical Centre, Mainz, Germany
| | - Yongqiang Feng
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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47564
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A Two-Component Regulatory System Impacts Extracellular Membrane-Derived Vesicle Production in Group A Streptococcus. mBio 2016; 7:mBio.00207-16. [PMID: 27803183 PMCID: PMC5090034 DOI: 10.1128/mbio.00207-16] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Export of macromolecules via extracellular membrane-derived vesicles (MVs) plays an important role in the biology of Gram-negative bacteria. Gram-positive bacteria have also recently been reported to produce MVs; however, the composition and mechanisms governing vesiculogenesis in Gram-positive bacteria remain undefined. Here, we describe MV production in the Gram-positive human pathogen group A streptococcus (GAS), the etiological agent of necrotizing fasciitis and streptococcal toxic shock syndrome. M1 serotype GAS isolates in culture exhibit MV structures both on the cell wall surface and in the near vicinity of bacterial cells. A comprehensive analysis of MV proteins identified both virulence-associated protein substrates of the general secretory pathway in addition to "anchorless surface proteins." Characteristic differences in the contents, distributions, and fatty acid compositions of specific lipids between MVs and GAS cell membrane were also observed. Furthermore, deep RNA sequencing of vesicular RNAs revealed that GAS MVs contained differentially abundant RNA species relative to bacterial cellular RNA. MV production by GAS strains varied in a manner dependent on an intact two-component system, CovRS, with MV production negatively regulated by the system. Modulation of MV production through CovRS was found to be independent of both GAS cysteine protease SpeB and capsule biosynthesis. Our data provide an explanation for GAS secretion of macromolecules, including RNAs, lipids, and proteins, and illustrate a regulatory mechanism coordinating this secretory response. IMPORTANCE Group A streptococcus (GAS) is a Gram-positive bacterial pathogen responsible for more than 500,000 deaths annually. Establishment of GAS infection is dependent on a suite of proteins exported via the general secretory pathway. Here, we show that GAS naturally produces extracellular vesicles with a unique lipid composition that are laden with proteins and RNAs. Interestingly, both virulence-associated proteins and RNA species were found to be differentially abundant in vesicles relative to the bacteria. Furthermore, we show that genetic disruption of the virulence-associated two-component regulator CovRS leads to an increase in vesicle production. This study comprehensively describes the protein, RNA, and lipid composition of GAS-secreted MVs and alludes to a regulatory system impacting this process.
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47565
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Williams LM, Lago BA, McArthur AG, Raphenya AR, Pray N, Saleem N, Salas S, Paulson K, Mangar RS, Liu Y, Vo AH, Shavit JA. The transcription factor, Nuclear factor, erythroid 2 (Nfe2), is a regulator of the oxidative stress response during Danio rerio development. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 180:141-154. [PMID: 27716579 PMCID: PMC5274700 DOI: 10.1016/j.aquatox.2016.09.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/28/2016] [Accepted: 09/30/2016] [Indexed: 05/17/2023]
Abstract
Development is a complex and well-defined process characterized by rapid cell proliferation and apoptosis. At this stage in life, a developmentally young organism is more sensitive to toxicants as compared to an adult. In response to pro-oxidant exposure, members of the Cap'n'Collar (CNC) basic leucine zipper (b-ZIP) transcription factor family (including Nfe2 and Nfe2-related factors, Nrfs) activate the expression of genes whose protein products contribute to reduced toxicity. Here, we studied the role of the CNC protein, Nfe2, in the developmental response to pro-oxidant exposure in the zebrafish (Danio rerio). Following acute waterborne exposures to diquat or tert-buytlhydroperoxide (tBOOH) at one of three developmental stages, wildtype (WT) and nfe2 knockout (KO) embryos and larvae were morphologically scored and their transcriptomes sequenced. Early in development, KO animals suffered from hypochromia that was made more severe through exposure to pro-oxidants; this phenotype in the KO may be linked to decreased expression of alas2, a gene involved in heme synthesis. WT and KO eleutheroembryos and larvae were phenotypically equally affected by exposure to pro-oxidants, where tBOOH caused more pronounced phenotypes as compared to diquat. Comparing diquat and tBOOH exposed embryos relative to the WT untreated control, a greater number of genes were up-regulated in the tBOOH condition as compared to diquat (tBOOH: 304 vs diquat: 148), including those commonly found to be differentially regulated in the vertebrate oxidative stress response (OSR) (e.g. hsp70.2, txn1, and gsr). When comparing WT and KO across all treatments and times, there were 1170 genes that were differentially expressed, of which 33 are known targets of the Nrf proteins Nrf1 and Nrf2. More specifically, in animals exposed to pro-oxidants a total of 968 genes were differentially expressed between WT and KO across developmental time, representing pathways involved in coagulation, embryonic organ development, body fluid level regulation, erythrocyte differentiation, and oxidation-reduction, amongst others. The greatest number of genes that changed in expression between WT and KO occurred in animals exposed to diquat at 2h post fertilization (hpf). Across time and treatment, there were six genes (dhx40, cfap70, dnajb9b, slc35f4, spi-c, and gpr19) that were significantly up-regulated in KO compared to WT and four genes (fhad1, cyp4v7, nlrp12, and slc16a6a) that were significantly down-regulated. None of these genes have been previously identified as targets of Nfe2 or the Nrf family. These results demonstrate that the zebrafish Nfe2 may be a regulator of both primitive erythropoiesis and the OSR during development.
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Affiliation(s)
- Larissa M Williams
- Biology Department, Bates College, 44 Campus Avenue, Lewiston, ME 04240, USA; The MDI Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609 USA, USA.
| | - Briony A Lago
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Andrew G McArthur
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Amogelang R Raphenya
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Nicholas Pray
- Biology Department, Bates College, 44 Campus Avenue, Lewiston, ME 04240, USA.
| | - Nabil Saleem
- Biology Department, Bates College, 44 Campus Avenue, Lewiston, ME 04240, USA; The MDI Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609 USA, USA.
| | - Sophia Salas
- Biology Department, Bates College, 44 Campus Avenue, Lewiston, ME 04240, USA; The MDI Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609 USA, USA.
| | - Katherine Paulson
- Biology Department, Bates College, 44 Campus Avenue, Lewiston, ME 04240, USA; The MDI Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609 USA, USA.
| | - Roshni S Mangar
- The MDI Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609 USA, USA; College of the Atlantic, 105 Eden Street, Bar Harbor, ME 04609, USA.
| | - Yang Liu
- Department of Pediatrics and Communicable Diseases, University of Michigan, 8200 MSRB III 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA.
| | - Andy H Vo
- Department of Pediatrics and Communicable Diseases, University of Michigan, 8200 MSRB III 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA.
| | - Jordan A Shavit
- Department of Pediatrics and Communicable Diseases, University of Michigan, 8200 MSRB III 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA.
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47566
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Sprenger H, Kurowsky C, Horn R, Erban A, Seddig S, Rudack K, Fischer A, Walther D, Zuther E, Köhl K, Hincha DK, Kopka J. The drought response of potato reference cultivars with contrasting tolerance. PLANT, CELL & ENVIRONMENT 2016; 39:2370-2389. [PMID: 27341794 DOI: 10.1111/pce.12780] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 05/21/2023]
Abstract
Systems responses to drought stress of four potato reference cultivars with differential drought tolerance (Solanum tuberosum L.) were investigated by metabolome profiling and RNA sequencing. Systems analysis was based on independent field and greenhouse trials. Robust differential drought responses across all cultivars under both conditions comprised changes of proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid and 102 transcript levels. The encoded genes contained a high proportion of heat shock proteins and proteins with signalling or regulatory functions, for example, a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant compared with the sensitive cultivars included arbutin, octopamine, ribitol and 248 transcripts. The gene products of many of these transcripts were pathogen response related, such as receptor kinases, or regulatory proteins, for example, a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply heat stress as a major acclimation component of potato leaves to long-term drought stress. Enhanced heat stress during drought can be caused by loss of transpiration cooling. This effect and CO2 limitation are the main consequences of drought-induced or abscisic acid-induced stomatal closure. Constitutive differences in metabolite and transcript levels between tolerant and sensitive cultivars indicate interactions of drought tolerance and pathogen resistance in potato.
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Affiliation(s)
- Heike Sprenger
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Christina Kurowsky
- Institut für Biowissenschaften und Pflanzengenetik, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
| | - Renate Horn
- Institut für Biowissenschaften und Pflanzengenetik, University of Rostock, Albert-Einstein-Straße 3, D-18059, Rostock, Germany
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Sylvia Seddig
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn Institut, Federal Research Centre for Cultivated Plants, Rudolf-Schick-Platz 3, D-18190, Sanitz, Germany
| | - Katharina Rudack
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn Institut, Federal Research Centre for Cultivated Plants, Rudolf-Schick-Platz 3, D-18190, Sanitz, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Karin Köhl
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Dirk K Hincha
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Golm, Potsdam, Germany.
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47567
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Mossanen JC, Krenkel O, Ergen C, Govaere O, Liepelt A, Puengel T, Heymann F, Kalthoff S, Lefebvre E, Eulberg D, Luedde T, Marx G, Strassburg CP, Roskams T, Trautwein C, Tacke F. Chemokine (C-C motif) receptor 2-positive monocytes aggravate the early phase of acetaminophen-induced acute liver injury. Hepatology 2016; 64:1667-1682. [PMID: 27302828 DOI: 10.1002/hep.28682] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/09/2016] [Accepted: 05/25/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Acetaminophen (APAP, paracetamol) poisoning is a leading cause of acute liver failure (ALF) in humans and induces hepatocyte necrosis, followed by activation of the innate immune system, further aggravating liver injury. The role of infiltrating monocytes during the early phase of ALF is still ambiguous. Upon experimental APAP overdose in mice, monocyte-derived macrophages (MoMFs) massively accumulated in injured liver within 12-24 hours, whereas the number of tissue-resident macrophages (Kupffer cells) decreased. Influx of MoMFs is dependent on the chemokine receptor, chemokine (C-C motif) receptor 2 (CCR2), given that Ccr2-/- mice display reduced infiltration of monocytes and attenuated liver injury post-APAP overdose at early time points. As evidenced by intravital multiphoton microscopy of Ccr2 reporter mice, CCR2+ monocytes infiltrate liver as early as 8-12 hours post-APAP overdose and form dense cellular clusters around necrotic areas. CCR2+ MoMFs express a distinct pattern of inflammatory, but also repair-associated, genes in injured livers. Adoptive transfer experiments revealed that MoMFs primarily exert proinflammatory functions early post-APAP, thereby aggravating liver injury. Consequently, early pharmacological inhibition of either chemokine (C-C motif) ligand (CCL2; by the inhibitor, mNOX-E36) or CCR2 (by the orally available dual CCR2/CCR5 inhibitor, cenicriviroc) reduces monocyte infiltration and APAP-induced liver injury (AILI) in mice. Importantly, neither the early nor continuous inhibition of CCR2 hinder repair processes during resolution from injury. In line with this, human livers of ALF patients requiring liver transplantation reveal increased CD68+ hepatic macrophage numbers with massive infiltrates of periportal CCR2+ macrophages that display a proinflammatory polarization. CONCLUSION Infiltrating monocyte-derived macrophages aggravate APAP hepatotoxicity, and the pharmacological inhibition of either CCL2 or CCR2 might bear therapeutic potential by reducing the inflammatory reaction during the early phase of AILI. (Hepatology 2016;64:1667-1682).
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Affiliation(s)
- Jana C Mossanen
- Department of Medicine III, University Hospital Aachen, Aachen, Germany.,Department of Intensive and Intermediate Care, University Hospital Aachen, Aachen, Germany
| | - Oliver Krenkel
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Can Ergen
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Olivier Govaere
- Department of Imaging & Pathology, University of Leuven, Leuven, Belgium
| | - Anke Liepelt
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Tobias Puengel
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Felix Heymann
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Sandra Kalthoff
- Department of Medicine I, University Hospital Bonn, Bonn, Germany
| | | | | | - Tom Luedde
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Gernot Marx
- Department of Intensive and Intermediate Care, University Hospital Aachen, Aachen, Germany
| | | | - Tania Roskams
- Department of Imaging & Pathology, University of Leuven, Leuven, Belgium
| | | | - Frank Tacke
- Department of Medicine III, University Hospital Aachen, Aachen, Germany.
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47568
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Barutcu AR, Hong D, Lajoie BR, McCord RP, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS. RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:1389-1397. [PMID: 27514584 PMCID: PMC5071180 DOI: 10.1016/j.bbagrm.2016.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023]
Abstract
RUNX1 is a transcription factor functioning both as an oncogene and a tumor suppressor in breast cancer. RUNX1 alters chromatin structure in cooperation with chromatin modifier and remodeling enzymes. In this study, we examined the relationship between RUNX1-mediated transcription and genome organization. We characterized genome-wide RUNX1 localization and performed RNA-seq and Hi-C in RUNX1-depleted and control MCF-7 breast cancer cells. RNA-seq analysis showed that RUNX1 depletion led to up-regulation of genes associated with chromatin structure and down-regulation of genes related to extracellular matrix biology, as well as NEAT1 and MALAT1 lncRNAs. Our ChIP-Seq analysis supports a prominent role for RUNX1 in transcriptional activation. About 30% of all RUNX1 binding sites were intergenic, indicating diverse roles in promoter and enhancer regulation and suggesting additional functions for RUNX1. Hi-C analysis of RUNX1-depleted cells demonstrated that overall three-dimensional genome organization is largely intact, but indicated enhanced association of RUNX1 near Topologically Associating Domain (TAD) boundaries and alterations in long-range interactions. These results suggest an architectural role for RUNX1 in fine-tuning local interactions rather than in global organization. Our results provide novel insight into RUNX1-mediated perturbations of higher-order genome organization that are functionally linked with RUNX1-dependent compromised gene expression in breast cancer cells.
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Affiliation(s)
- A Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Deli Hong
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Bryan R Lajoie
- Program in Systems Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Rachel Patton McCord
- Program in Systems Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Andre J van Wijnen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Jane B Lian
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L Stein
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
| | - Gary S Stein
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA.
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47569
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Charrier A, Wang L, Stephenson EJ, Ghanta SV, Ko CW, Croniger CM, Bridges D, Buchner DA. Zinc finger protein 407 overexpression upregulates PPAR target gene expression and improves glucose homeostasis in mice. Am J Physiol Endocrinol Metab 2016; 311:E869-E880. [PMID: 27624101 PMCID: PMC5130358 DOI: 10.1152/ajpendo.00234.2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/16/2016] [Accepted: 09/10/2016] [Indexed: 01/13/2023]
Abstract
The peroxisome proliferator-activated receptor (PPAR) family of nuclear receptors is central to the pathophysiology and treatment of metabolic disease through the receptors' ability to regulate the expression of genes involved in glucose homeostasis, adipogenesis, and lipid metabolism. However, the mechanism by which PPAR is regulated remains incompletely understood. We generated a transgenic mouse strain (ZFP-TG) that overexpressed Zfp407 primarily in muscle and heart. Transcriptome analysis by RNA-Seq identified 1,300 differentially expressed genes in the muscle of ZFP-TG mice, among which PPAR target genes were significantly enriched. Among the physiologically important PPARγ target genes, Glucose transporter (Glut)-4 mRNA and protein levels were increased in heart and muscle. The increase in Glut4 and other transcriptional effects of Zfp407 overexpression together decreased body weight and lowered plasma glucose, insulin, and HOMA-IR scores relative to control littermates. When placed on high-fat diet, ZFP-TG mice remained more glucose tolerant than their wild-type counterparts. Cell-based assays demonstrated that Zfp407 synergistically increased the transcriptional activity of all PPAR subtypes, PPARα, PPARγ, and PPARδ. The increased PPAR activity was not associated with increased PPAR mRNA or protein levels, suggesting that Zfp407 posttranslationally regulates PPAR activity. Collectively, these results demonstrate that Zfp407 overexpression improved glucose homeostasis. Thus, Zfp407 represents a new drug target for treating metabolic disease.
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Affiliation(s)
- Alyssa Charrier
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Li Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Erin J Stephenson
- Departments of Physiology and Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Siddharth V Ghanta
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio; and
| | - Chih-Wei Ko
- Department of Nutrition, Case Western Reserve University, Cleveland, Ohio
| | - Colleen M Croniger
- Department of Nutrition, Case Western Reserve University, Cleveland, Ohio
| | - Dave Bridges
- Departments of Physiology and Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
| | - David A Buchner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio;
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio; and
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47570
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Zambetti N, Ping Z, Chen S, Kenswil K, Mylona M, Sanders M, Hoogenboezem R, Bindels E, Adisty M, Van Strien P, van der Leije C, Westers T, Cremers E, Milanese C, Mastroberardino P, van Leeuwen J, van der Eerden B, Touw I, Kuijpers T, Kanaar R, van de Loosdrecht A, Vogl T, Raaijmakers M. Mesenchymal Inflammation Drives Genotoxic Stress in Hematopoietic Stem Cells and Predicts Disease Evolution in Human Pre-leukemia. Cell Stem Cell 2016; 19:613-627. [DOI: 10.1016/j.stem.2016.08.021] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 07/06/2016] [Accepted: 08/22/2016] [Indexed: 12/22/2022]
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47571
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Agnihotri S, Jalali S, Wilson MR, Danesh A, Li M, Klironomos G, Krieger JR, Mansouri A, Khan O, Mamatjan Y, Landon-Brace N, Tung T, Dowar M, Li T, Bruce JP, Burrell KE, Tonge PD, Alamsahebpour A, Krischek B, Agarwalla PK, Bi WL, Dunn IF, Beroukhim R, Fehlings MG, Bril V, Pagnotta SM, Iavarone A, Pugh TJ, Aldape KD, Zadeh G. The genomic landscape of schwannoma. Nat Genet 2016; 48:1339-1348. [PMID: 27723760 DOI: 10.1038/ng.3688] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/02/2016] [Indexed: 12/13/2022]
Abstract
Schwannomas are common peripheral nerve sheath tumors that can cause debilitating morbidities. We performed an integrative analysis to determine genomic aberrations common to sporadic schwannomas. Exome sequence analysis with validation by targeted DNA sequencing of 125 samples uncovered, in addition to expected NF2 disruption, recurrent mutations in ARID1A, ARID1B and DDR1. RNA sequencing identified a recurrent in-frame SH3PXD2A-HTRA1 fusion in 12/125 (10%) cases, and genomic analysis demonstrated the mechanism as resulting from a balanced 19-Mb chromosomal inversion on chromosome 10q. The fusion was associated with male gender predominance, occurring in one out of every six men with schwannoma. Methylation profiling identified distinct molecular subgroups of schwannomas that were associated with anatomical location. Expression of the SH3PXD2A-HTRA1 fusion resulted in elevated phosphorylated ERK, increased proliferation, increased invasion and in vivo tumorigenesis. Targeting of the MEK-ERK pathway was effective in fusion-positive Schwann cells, suggesting a possible therapeutic approach for this subset of tumors.
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MESH Headings
- Adaptor Proteins, Vesicular Transport/genetics
- Animals
- Cell Line, Tumor
- DNA Methylation
- DNA Mutational Analysis
- DNA, Neoplasm
- Ear Neoplasms/genetics
- Exome
- Female
- Gene Fusion
- Genome, Human
- High-Temperature Requirement A Serine Peptidase 1
- Humans
- Male
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Mutation
- Neurilemmoma/genetics
- RNA, Neoplasm
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- Serine Endopeptidases/genetics
- Spinal Neoplasms/genetics
- Vestibule, Labyrinth
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Affiliation(s)
- Sameer Agnihotri
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shahrzad Jalali
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark R Wilson
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mira Li
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - George Klironomos
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jonathan R Krieger
- SPARC Biocentre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alireza Mansouri
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Osaama Khan
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Natalie Landon-Brace
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Takyee Tung
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark Dowar
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kelly E Burrell
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter D Tonge
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Amir Alamsahebpour
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Boris Krischek
- Department of Neurosurgery, University Hospital of Cologne, Cologne Germany
| | - Pankaj Kumar Agarwalla
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Wenya Linda Bi
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ian F Dunn
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Rameen Beroukhim
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michael G Fehlings
- Department of Neurosurgery, University Health Network, Toronto, Ontario, Canada
| | - Vera Bril
- Department of Medicine (Neurology), and the Elizabeth Raab Neurofibromatosis Program, University of Toronto, Toronto, Ontario, Canada
| | - Stefano M Pagnotta
- Department of Science and Technology, Università degli Studi del Sannio, Benevento, Italy
- Department of Pathology and Cell Biology and Neurology, Columbia University, New York, New York, USA
| | - Antonio Iavarone
- Department of Pathology and Cell Biology and Neurology, Columbia University, New York, New York, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth D Aldape
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, Maryland Anderson Cancer Center, Houston, Texas, USA
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Neurosurgery, University Health Network, Toronto, Ontario, Canada
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47572
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Sánchez CA, Andahur EI, Valenzuela R, Castellón EA, Fullá JA, Ramos CG, Triviño JC. Exosomes from bulk and stem cells from human prostate cancer have a differential microRNA content that contributes cooperatively over local and pre-metastatic niche. Oncotarget 2016; 7:3993-4008. [PMID: 26675257 PMCID: PMC4826185 DOI: 10.18632/oncotarget.6540] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/25/2015] [Indexed: 01/01/2023] Open
Abstract
The different prostate cancer (PCa) cell populations (bulk and cancer stem cells, CSCs) release exosomes that contain miRNAs that could modify the local or premetastatic niche. The analysis of the differential expression of miRNAs in exosomes allows evaluating the differential biological effect of both populations on the niche, and the identification of potential biomarkers and therapeutic targets. Five PCa primary cell cultures were established to originate bulk and CSCs cultures. From them, exosomes were purified by precipitation for miRNAs extraction to perform a comparative profile of miRNAs by next generation sequencing in an Illumina platform. 1839 miRNAs were identified in the exosomes. Of these 990 were known miRNAs, from which only 19 were significantly differentially expressed: 6 were overexpressed in CSCs and 13 in bulk cells exosomes. miR-100-5p and miR-21-5p were the most abundant miRNAs. Bioinformatics analysis indicated that differentially expressed miRNAs are highly related with PCa carcinogenesis, fibroblast proliferation, differentiation and migration, and angiogenesis. Besides, miRNAs from bulk cells affects osteoblast differentiation. Later, their effect was evaluated in normal prostate fibroblasts (WPMY-1) where transfection with miR-100-5p, miR-21-5p and miR-139-5p increased the expression of metalloproteinases (MMPs) -2, -9 and -13 and RANKL and fibroblast migration. The higher effect was achieved with miR21 transfection. As conclusion, miRNAs have a differential pattern between PCa bulk and CSCs exosomes that act collaboratively in PCa progression and metastasis. The most abundant miRNAs in PCa exosomes are interesting potential biomarkers and therapeutic targets.
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Affiliation(s)
| | - Eliana I Andahur
- Urology Department, Las Condes Clinic, Santiago, Chile.,Faculty of Science, University of Chile, Santiago, Chile
| | | | | | - Juan A Fullá
- Urology Department, Las Condes Clinic, Santiago, Chile
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47573
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Van Aken O, Ford E, Lister R, Huang S, Millar AH. Retrograde signalling caused by heritable mitochondrial dysfunction is partially mediated by ANAC017 and improves plant performance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:542-558. [PMID: 27425258 DOI: 10.1111/tpj.13276] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 06/06/2023]
Abstract
Mitochondria are crucial for plant viability and are able to communicate information on their functional status to the cellular nucleus via retrograde signalling, thereby affecting gene expression. It is currently unclear if retrograde signalling in response to constitutive mitochondrial biogenesis defects is mediated by the same pathways as those triggered during acute mitochondrial dysfunction. Furthermore, it is unknown if retrograde signalling can effectively improve plant performance when mitochondrial function is constitutively impaired. Here we show that retrograde signalling in mutants defective in mitochondrial proteins RNA polymerase rpotmp or prohibitin atphb3 can be suppressed by knocking out the transcription factor ANAC017. Genome-wide RNA-seq expression analysis revealed that ANAC017 is almost solely responsible for the most dramatic transcriptional changes common to rpotmp and atphb3 mutants, regulating classical marker genes such as alternative oxidase 1a (AOX1a) and also previously-uncharacterised DUF295 genes that appear to be new retrograde markers. In contrast, ANAC017 does not regulate intra-mitochondrial gene expression or transcriptional changes unique to either rpotmp or atphb3 genotype, suggesting the existence of currently unknown signalling cascades. The data show that ANAC017 function extends beyond common retrograde transcriptional responses and affects downstream protein abundance and enzyme activity of alternative oxidase, as well as steady-state energy metabolism in atphb3 plants. Furthermore, detailed growth analysis revealed that ANAC017-dependent retrograde signalling provides benefits for growth and productivity in plants with mitochondrial defects. In conclusion, ANAC017 plays a key role in both biogenic and operational mitochondrial retrograde signalling, and improves plant performance when mitochondrial function is constitutively impaired.
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Affiliation(s)
- Olivier Van Aken
- Faculty of Science, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Ethan Ford
- Faculty of Science, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Ryan Lister
- Faculty of Science, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Shaobai Huang
- Faculty of Science, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - A Harvey Millar
- Faculty of Science, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
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47574
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Wang Y, Galivo F, Pelz C, Haft A, Lee J, Kim SK, Grompe M. Efficient generation of pancreatic β-like cells from the mouse gallbladder. Stem Cell Res 2016; 17:587-596. [PMID: 27833043 DOI: 10.1016/j.scr.2016.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/17/2016] [Accepted: 10/25/2016] [Indexed: 12/18/2022] Open
Abstract
Direct reprogramming is a promising approach for the replacement of β cells in diabetes. Reprogramming of cells originating from the endodermal lineage, such as acinar cells in the pancreas, liver cells and gallbladder cells has been of particular interest because of their developmental proximity to β cells. Our previous work showed that mouse gallbladder epithelium can be partially reprogrammed in vitro to generate islet-like cells (rGBC1). Here, the reprogramming protocol was substantially improved, yielding cells (rGBC2) closer to functional β cells than the 1st generation method with higher conversion efficiency and insulin expression. In addition to insulin synthesis and processing, rGBC2 presented many hallmark features of β cells, including insulin secretion in response to high glucose stimulation. Gene expression analysis indicated that rGBC2 clustered closer with β cells and had a metabolic gene expression profile resembling neonatal β cells. When transplanted into immune-deficient animals, rGBC2 were stable for at least 5months and further matured in vivo. Taken together, this approach provides further understanding of endodermal lineage conversion and potential for development of cell replacement therapy for type 1 diabetes patients.
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Affiliation(s)
- Yuhan Wang
- Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Feorillo Galivo
- Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Carl Pelz
- Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Annelise Haft
- Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jonghyeob Lee
- Department of Developmental Biology, Department of Medicine (Division of Oncology), Stanford University School of Medicine, Stanford, CA, USA
| | - Seung K Kim
- Department of Developmental Biology, Department of Medicine (Division of Oncology), Stanford University School of Medicine, Stanford, CA, USA
| | - Markus Grompe
- Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.
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47575
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Pumplin N, Sarazin A, Jullien PE, Bologna NG, Oberlin S, Voinnet O. DNA Methylation Influences the Expression of DICER-LIKE4 Isoforms, Which Encode Proteins of Alternative Localization and Function. THE PLANT CELL 2016; 28:2786-2804. [PMID: 27956586 PMCID: PMC5155348 DOI: 10.1105/tpc.16.00554] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/21/2016] [Accepted: 11/12/2016] [Indexed: 05/08/2023]
Abstract
Plant RNA silencing operates via RNA-directed DNA-methylation (RdDM) to repress transcription or by targeting mRNAs via posttranscriptional gene silencing (PTGS). These pathways rely on distinct Dicer-like (DCL) proteins that process double-stranded RNA (dsRNA) into small-interfering RNAs (siRNAs). Here, we explored the expression and subcellular localization of Arabidopsis thaliana DCL4. DCL4 expression predominates as a transcription start site isoform encoding a cytoplasmic protein, which also represents the ancestral form in plants. A longer DCL4 transcript isoform encoding a nuclear localization signal, DCL4NLS, is present in Arabidopsis, but DNA methylation normally suppresses its expression. Hypomethylation caused by mutation, developmental reprogramming, and biotic stress correlates with enhanced DCL4NLS expression, while hypermethylation of a DCL4 transgene causes a reduction in DCL4NLS expression. DCL4NLS functions in a noncanonical siRNA pathway, producing a unique set of 21-nucleotide-long "disiRNAs," for DCL4NLS isoform-dependent siRNAs, through the nuclear RdDM dsRNA synthesis pathway. disiRNAs originate mostly from transposable elements (TEs) and TE-overlapping/proximal genes, load into the PTGS effector ARGONAUTE1 (AGO1), and display a subtle effect on transcript accumulation together with overlapping 24-nucleotide siRNAs. We propose that, via PTGS, disiRNAs could help to tighten the expression of epigenetically activated TEs and genes using the methylation-state-responsive DCL4NLS.
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Affiliation(s)
- Nathan Pumplin
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Alexis Sarazin
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | | | | | - Stefan Oberlin
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
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47576
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Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. THE PLANT CELL 2016; 28:2700-2714. [PMID: 27803309 PMCID: PMC5155341 DOI: 10.1105/tpc.16.00353] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 05/18/2023]
Abstract
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.
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Affiliation(s)
- Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Megan J Bowman
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Ilya Soifer
- Calico Labs, San Francisco, California 94080
| | | | | | | | - Fei Lu
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Christopher J Fields
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Chris L Wright
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | | | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Edward Buckler
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
- U.S. Department of Agriculture/Agricultural Research Services, Ithaca, New York 14850
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- DOE Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Center for Genomics-Enabled Plant Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Mark A Mikel
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
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47577
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Jackman JG, Juwarker H, Poveromo LP, Levinson H, Leong KW, Sullenger BA. Polycationic Nanofibers for Nucleic Acid Scavenging. Biomacromolecules 2016; 17:3706-3713. [PMID: 27741396 DOI: 10.1021/acs.biomac.6b01236] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Dying cells release nucleic acids (NA) and NA-containing complexes that activate inflammatory pathways of immune cells. Sustained activation of these pathways contributes to chronic inflammation frequently encountered in autoimmune and inflammatory diseases. In this study, grafting of cationic polymers onto a nanofibrous mesh enabled local scavenging of negatively charged pro-inflammatory molecules in the extracellular space. Nucleic acid scavenging nanofibers (NASFs) formed from poly(styrene-alt-maleic anhydride) conjugated with 1.8 kDa bPEI resulted in nanofibers of diameters 486 ± 9 nm. NASFs inhibited the NF-κB response stimulated by the negatively charged agonists, CpG and poly(I:C), in Ramos-blue cells but not Pam3CSK4, a nonanionic agonist. Moreover, NASFs significantly impeded NF-κB activation in cells stimulated with damage-associated molecular pattern molecules (DAMPs) released from doxorubicin killed cancer cells. In vivo application of NASFs to open wounds demonstrated nucleic acid scavenging in wounds of diabetic mice infected with Pseudomonas aeruginosa, suggesting the in vivo efficacy of NASFs. This simple technique of generating NASF results in effective localized anti-inflammation in vitro and local nucleic acid scavenging in vivo.
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Affiliation(s)
| | | | | | | | - Kam W Leong
- Department of Biomedical Engineering, Columbia University , New York, New York, United States
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47578
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Zhu S, Li W, Liu J, Chen CH, Liao Q, Xu P, Xu H, Xiao T, Cao Z, Peng J, Yuan P, Brown M, Liu XS, Wei W. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat Biotechnol 2016; 34:1279-1286. [PMID: 27798563 DOI: 10.1038/nbt.3715] [Citation(s) in RCA: 311] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 09/30/2016] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas9 screens have been widely adopted to analyze coding-gene functions, but high-throughput screening of non-coding elements using this method is more challenging because indels caused by a single cut in non-coding regions are unlikely to produce a functional knockout. A high-throughput method to produce deletions of non-coding DNA is needed. We report a high-throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library. Applying our screening method, we identified 51 lncRNAs that can positively or negatively regulate human cancer cell growth. We validated 9 of 51 lncRNA hits using CRISPR-Cas9-mediated genomic deletion, functional rescue, CRISPR activation or inhibition and gene-expression profiling. Our high-throughput pgRNA genome deletion method will enable rapid identification of functional mammalian non-coding elements.
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Affiliation(s)
- Shiyou Zhu
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China
| | - Wei Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jingze Liu
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China
| | - Chen-Hao Chen
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Qi Liao
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Ping Xu
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Han Xu
- Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, Massachusetts, USA
| | - Tengfei Xiao
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Zhongzheng Cao
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jingyu Peng
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Pengfei Yuan
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaole Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Wensheng Wei
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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47579
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O'Brien VP, Hannan TJ, Yu L, Livny J, Roberson EDO, Schwartz DJ, Souza S, Mendelsohn CL, Colonna M, Lewis AL, Hultgren SJ. A mucosal imprint left by prior Escherichia coli bladder infection sensitizes to recurrent disease. Nat Microbiol 2016; 2:16196. [PMID: 27798558 DOI: 10.1038/nmicrobiol.2016.196] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/07/2016] [Indexed: 01/26/2023]
Abstract
Recurrent bacterial infections are a significant burden worldwide, and prior history of infection is often a significant risk factor for developing new infections. For urinary tract infection (UTI), a history of two or more episodes is an independent risk factor for acute infection. However, mechanistic knowledge of UTI pathogenesis has come almost exclusively from studies in naive mice. Here we show that, in mice, an initial Escherichia coli UTI, whether chronic or self-limiting, leaves a long-lasting molecular imprint on the bladder tissue that alters the pathophysiology of subsequent infections, affecting host susceptibility and disease outcome. In bladders of previously infected versus non-infected, antibiotic-treated mice, we found (1) an altered transcriptome and defects in cell maturation, (2) a remodelled epithelium that confers resistance to intracellular bacterial colonization, and (3) changes to cyclooxygenase-2-dependent inflammation. Furthermore, in mice with a history of chronic UTI, cyclooxygenase-2-dependent inflammation allowed a variety of clinical E. coli isolates to circumvent intracellular colonization resistance and cause severe recurrent UTI, which could be prevented by cyclooxygenase-2 inhibition or vaccination. This work provides mechanistic insight into how a history of infection can impact the risk for developing recurrent infection and has implications for the development of therapeutics for recurrent UTI.
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Affiliation(s)
- Valerie P O'Brien
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Thomas J Hannan
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Lu Yu
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Jonathan Livny
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Elisha D O Roberson
- Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St Louis, Missouri 63110, USA.,Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Drew J Schwartz
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Spenser Souza
- Departments of Urology and Genetics &Development, Columbia University, New York, New York 10032, USA
| | - Cathy L Mendelsohn
- Departments of Urology and Genetics &Development, Columbia University, New York, New York 10032, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Amanda L Lewis
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri 63110, USA.,Department of Obstetrics and Gynecology, Washington University School of Medicine, St Louis 63110, Missouri, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri 63110, USA
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47580
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Pitt FD, Millard A, Ostrowski M, Dervish S, Mazard S, Paulsen IT, Zubkov MV, Scanlan DJ. A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus. Front Microbiol 2016; 7:1592. [PMID: 27790194 PMCID: PMC5063861 DOI: 10.3389/fmicb.2016.01592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/22/2016] [Indexed: 12/02/2022] Open
Abstract
Recent studies using whole community metagenomic and metatranscriptomic approaches are revealing important new insights into the functional potential and activity of natural marine microbial communities. Here, we complement these approaches by describing a complete ocean sample-to-sequence protocol, specifically designed to target a single bacterial genus for purposes of both DNA and RNA profiling using fluorescence activated cell sorting (FACS). The importance of defining and understanding the effects of a sampling protocol are critical if we are to gain meaningful data from environmental surveys. Rigorous pipeline trials with a cultured isolate, Synechococcus sp. BL107 demonstrate that water filtration has a well-defined but limited impact on the transcriptomic profile of this organism, whilst sample storage and multiple rounds of cell sorting have almost no effect on the resulting RNA sequence profile. Attractively, the means to replicate the sampling strategy is within the budget and expertise of most researchers.
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Affiliation(s)
- Frances D Pitt
- School of Life Sciences, University of Warwick Coventry, UK
| | - Andrew Millard
- Warwick Medical School, University of Warwick Coventry, UK
| | - Martin Ostrowski
- Department of Biochemistry and Biomolecular Science, Faculty of Science and Engineering, Macquarie University Sydney, NSW, Australia
| | - Suat Dervish
- Sydney Cytometry, Centenary Institute, University of Sydney Sydney, NSW, Australia
| | - Sophie Mazard
- Department of Biochemistry and Biomolecular Science, Faculty of Science and Engineering, Macquarie University Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Biochemistry and Biomolecular Science, Faculty of Science and Engineering, Macquarie University Sydney, NSW, Australia
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47581
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Dietary Gluten-Induced Gut Dysbiosis Is Accompanied by Selective Upregulation of microRNAs with Intestinal Tight Junction and Bacteria-Binding Motifs in Rhesus Macaque Model of Celiac Disease. Nutrients 2016; 8:nu8110684. [PMID: 27801835 PMCID: PMC5133072 DOI: 10.3390/nu8110684] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 12/15/2022] Open
Abstract
The composition of the gut microbiome reflects the overall health status of the host. In this study, stool samples representing the gut microbiomes from 6 gluten-sensitive (GS) captive juvenile rhesus macaques were compared with those from 6 healthy, age- and diet-matched peers. A total of 48 samples representing both groups were studied using V4 16S rRNA gene DNA analysis. Samples from GS macaques were further characterized based on type of diet administered: conventional monkey chow, i.e., wheat gluten-containing diet (GD), gluten-free diet (GFD), barley gluten-derived diet (BOMI) and reduced gluten barley-derived diet (RGB). It was hypothesized that the GD diet would lower the gut microbial diversity in GS macaques. This is the first report illustrating the reduction of gut microbial alpha-diversity (p < 0.05) following the consumption of dietary gluten in GS macaques. Selected bacterial families (e.g., Streptococcaceae and Lactobacillaceae) were enriched in GS macaques while Coriobacteriaceae was enriched in healthy animals. Within several weeks after the replacement of the GD by the GFD diet, the composition (beta-diversity) of gut microbiome in GS macaques started to change (p = 0.011) towards that of a normal macaque. Significance for alpha-diversity however, was not reached by the day 70 when the feeding experiment ended. Several inflammation-associated microRNAs (miR-203, -204, -23a, -23b and -29b) were upregulated (p < 0.05) in jejunum of 4 biopsied GS macaques fed GD with predicted binding sites on 16S ribosomal RNA of Lactobacillus reuteri (accession number: NR_025911), Prevotella stercorea (NR_041364) and Streptococcus luteciae (AJ297218) that were overrepresented in feces. Additionally, claudin-1, a validated tight junction protein target of miR-29b was significantly downregulated in jejunal epithelium of GS macaques. Taken together, we predict that with the introduction of effective treatments in future studies the diversity of gut microbiomes in GS macaques will approach those of healthy individuals. Further studies are needed to elucidate the regulatory pathways of inflammatory miRNAs in intestinal mucosa of GS macaques and to correlate their expression with gut dysbiosis.
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47582
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Karna SLR, D’Arpa P, Chen T, Qian LW, Fourcaudot AB, Yamane K, Chen P, Abercrombie JJ, You T, Leung KP. RNA-Seq Transcriptomic Responses of Full-Thickness Dermal Excision Wounds to Pseudomonas aeruginosa Acute and Biofilm Infection. PLoS One 2016; 11:e0165312. [PMID: 27792773 PMCID: PMC5085052 DOI: 10.1371/journal.pone.0165312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/10/2016] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa infections of wounds in clinical settings are major complications whose outcomes are influenced by host responses that are not completely understood. Herein we evaluated transcriptomic changes of wounds as they counter P. aeruginosa infection—first active infection, and then chronic biofilm infection. We used the dermal full-thickness, rabbit ear excisional wound model. We studied the wound response: towards acute infection at 2, 6, and 24 hrs after inoculating 106 bacteria into day-3 wounds; and, towards more chronic biofilm infection of wounds similarly infected for 24 hrs but then treated with topical antibiotic to coerce biofilm growth and evaluated at day 5 and 9 post-infection. The wounds were analyzed for bacterial counts, expression of P. aeruginosa virulence and biofilm-synthesis genes, biofilm morphology, infiltrating immune cells, re-epithelialization, and genome-wide gene expression (RNA-Seq transcriptome). This analysis revealed that 2 hrs after bacterial inoculation into day-3 wounds, the down-regulated genes (infected vs. non-infected) of the wound edge were nearly all non-coding RNAs (ncRNAs), comprised of snoRNA, miRNA, and RNU6 pseudogenes, and their down-regulation preceded a general down-regulation of skin-enriched coding gene expression. As the active infection intensified, ncRNAs remained overrepresented among down-regulated genes; however, at 6 and 24 hrs they changed to a different set, which overlapped between these times, and excluded RNU6 pseudogenes but included snRNA components of the major and minor spliceosomes. Additionally, the raw counts of multiple types of differentially-expressed ncRNAs increased on post-wounding day 3 in control wounds, but infection suppressed this increase. After 5 and 9 days, these ncRNA counts in control wounds decreased, whereas they increased in the infected, healing-impaired wounds. These data suggest a sequential and coordinated change in the levels of transcripts of multiple major classes of ncRNAs in wound cells transitioning from inflammation to the proliferation phase of healing.
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Affiliation(s)
- S. L. Rajasekhar Karna
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America
| | - Peter D’Arpa
- US Army Center for Environmental Health Research, Fort Detrick, Maryland, United States of America
- The Geneva Foundation, Tacoma, Washington, United States of America
| | - Tsute Chen
- The Forsyth Institute, Cambridge, Massachusetts, United States of America
| | - Li-Wu Qian
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America
| | - Andrea B. Fourcaudot
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America
| | - Kazuyoshi Yamane
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America
| | - Ping Chen
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America
| | - Johnathan J. Abercrombie
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America
| | - Tao You
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America
| | - Kai P. Leung
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America
- * E-mail:
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47583
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Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils. Appl Environ Microbiol 2016; 82:6518-6530. [PMID: 27590813 PMCID: PMC5086546 DOI: 10.1128/aem.02012-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 08/19/2016] [Indexed: 11/20/2022] Open
Abstract
As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.
IMPORTANCE The massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.
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47584
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Dai HQ, Wang BA, Yang L, Chen JJ, Zhu GC, Sun ML, Ge H, Wang R, Chapman DL, Tang F, Sun X, Xu GL. TET-mediated DNA demethylation controls gastrulation by regulating Lefty-Nodal signalling. Nature 2016; 538:528-532. [PMID: 27760115 DOI: 10.1038/nature20095] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 09/15/2016] [Indexed: 12/11/2022]
Abstract
Mammalian genomes undergo epigenetic modifications, including cytosine methylation by DNA methyltransferases (DNMTs). Oxidation of 5-methylcytosine by the Ten-eleven translocation (TET) family of dioxygenases can lead to demethylation. Although cytosine methylation has key roles in several processes such as genomic imprinting and X-chromosome inactivation, the functional significance of cytosine methylation and demethylation in mouse embryogenesis remains to be fully determined. Here we show that inactivation of all three Tet genes in mice leads to gastrulation phenotypes, including primitive streak patterning defects in association with impaired maturation of axial mesoderm and failed specification of paraxial mesoderm, mimicking phenotypes in embryos with gain-of-function Nodal signalling. Introduction of a single mutant allele of Nodal in the Tet mutant background partially restored patterning, suggesting that hyperactive Nodal signalling contributes to the gastrulation failure of Tet mutants. Increased Nodal signalling is probably due to diminished expression of the Lefty1 and Lefty2 genes, which encode inhibitors of Nodal signalling. Moreover, reduction in Lefty gene expression is linked to elevated DNA methylation, as both Lefty-Nodal signalling and normal morphogenesis are largely restored in Tet-deficient embryos when the Dnmt3a and Dnmt3b genes are disrupted. Additionally, a point mutation in Tet that specifically abolishes the dioxygenase activity causes similar morphological and molecular abnormalities as the null mutation. Taken together, our results show that TET-mediated oxidation of 5-methylcytosine modulates Lefty-Nodal signalling by promoting demethylation in opposition to methylation by DNMT3A and DNMT3B. These findings reveal a fundamental epigenetic mechanism featuring dynamic DNA methylation and demethylation crucial to regulation of key signalling pathways in early body plan formation.
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Affiliation(s)
- Hai-Qiang Dai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai 200031, China
| | - Bang-An Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai 200031, China
| | - Lu Yang
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking University, Beijing 100871, China
| | - Jia-Jia Chen
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai 200031, China
| | - Guo-Chun Zhu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai 200031, China
| | - Mei-Ling Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Hao Ge
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China
| | - Rui Wang
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking University, Beijing 100871, China
| | - Deborah L Chapman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Fuchou Tang
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking University, Beijing 100871, China
| | - Xin Sun
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
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47585
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Sen DR, Kaminski J, Barnitz RA, Kurachi M, Gerdemann U, Yates KB, Tsao HW, Godec J, LaFleur MW, Brown FD, Tonnerre P, Chung RT, Tully DC, Allen TM, Frahm N, Lauer GM, Wherry EJ, Yosef N, Haining WN. The epigenetic landscape of T cell exhaustion. Science 2016; 354:1165-1169. [PMID: 27789799 DOI: 10.1126/science.aae0491] [Citation(s) in RCA: 657] [Impact Index Per Article: 82.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 10/07/2016] [Indexed: 12/12/2022]
Abstract
Exhausted T cells in cancer and chronic viral infection express distinctive patterns of genes, including sustained expression of programmed cell death protein 1 (PD-1). However, the regulation of gene expression in exhausted T cells is poorly understood. Here, we define the accessible chromatin landscape in exhausted CD8+ T cells and show that it is distinct from functional memory CD8+ T cells. Exhausted CD8+ T cells in humans and a mouse model of chronic viral infection acquire a state-specific epigenetic landscape organized into functional modules of enhancers. Genome editing shows that PD-1 expression is regulated in part by an exhaustion-specific enhancer that contains essential RAR, T-bet, and Sox3 motifs. Functional enhancer maps may offer targets for genome editing that alter gene expression preferentially in exhausted CD8+ T cells.
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Affiliation(s)
- Debattama R Sen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - James Kaminski
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - R Anthony Barnitz
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Makoto Kurachi
- Institute of Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ulrike Gerdemann
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kathleen B Yates
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Hsiao-Wei Tsao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jernej Godec
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Martin W LaFleur
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Flavian D Brown
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Pierre Tonnerre
- Gastrointestinal Unit and Liver Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Raymond T Chung
- Gastrointestinal Unit and Liver Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Damien C Tully
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02139, USA
| | - Todd M Allen
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02139, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Georg M Lauer
- Gastrointestinal Unit and Liver Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - E John Wherry
- Institute of Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA. .,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02139, USA.,Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. .,Division of Pediatric Hematology and Oncology, Children's Hospital, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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47586
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Yau S, Hemon C, Derelle E, Moreau H, Piganeau G, Grimsley N. A Viral Immunity Chromosome in the Marine Picoeukaryote, Ostreococcus tauri. PLoS Pathog 2016; 12:e1005965. [PMID: 27788272 PMCID: PMC5082852 DOI: 10.1371/journal.ppat.1005965] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 09/29/2016] [Indexed: 12/22/2022] Open
Abstract
Micro-algae of the genus Ostreococcus and related species of the order Mamiellales are globally distributed in the photic zone of world's oceans where they contribute to fixation of atmospheric carbon and production of oxygen, besides providing a primary source of nutrition in the food web. Their tiny size, simple cells, ease of culture, compact genomes and susceptibility to the most abundant large DNA viruses in the sea render them attractive as models for integrative marine biology. In culture, spontaneous resistance to viruses occurs frequently. Here, we show that virus-producing resistant cell lines arise in many independent cell lines during lytic infections, but over two years, more and more of these lines stop producing viruses. We observed sweeping over-expression of all genes in more than half of chromosome 19 in resistant lines, and karyotypic analyses showed physical rearrangements of this chromosome. Chromosome 19 has an unusual genetic structure whose equivalent is found in all of the sequenced genomes in this ecologically important group of green algae. We propose that chromosome 19 of O. tauri is specialized in defence against viral attack, a constant threat for all planktonic life, and that the most likely cause of resistance is the over-expression of numerous predicted glycosyltransferase genes. O. tauri thus provides an amenable model for molecular analysis of genome evolution under environmental stress and for investigating glycan-mediated host-virus interactions, such as those seen in herpes, influenza, HIV, PBCV and mimivirus.
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Affiliation(s)
- Sheree Yau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Claire Hemon
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Evelyne Derelle
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Hervé Moreau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Gwenaël Piganeau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Nigel Grimsley
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
- * E-mail:
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47587
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Perazzolli M, Herrero N, Sterck L, Lenzi L, Pellegrini A, Puopolo G, Van de Peer Y, Pertot I. Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat. BMC Genomics 2016; 17:838. [PMID: 27784266 PMCID: PMC5081961 DOI: 10.1186/s12864-016-3174-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/18/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the microorganisms. RESULTS A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen (Armillaria mellea) and its biocontrol agent (Trichoderma atroviride) for 24 h under controlled conditions. More than 46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and neutral adaptation processes were activated in response to competitive (T. atroviride) or non-competitive (A. mellea) microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil microcosm in the presence of both A. mellea and T. atroviride. Biocontrol processes of T. atroviride were already activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem, and they were not further enhanced by the introduction of A. mellea. CONCLUSIONS This work represents an additional step towards understanding molecular interactions between plant pathogens and biocontrol agents within a soil ecosystem. Global transcriptional analysis of the simplified soil microcosm revealed complex metabolic adaptation in the soil environment and specific responses to antagonistic or neutral intruders.
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Affiliation(s)
- Michele Perazzolli
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige, Italy.
| | - Noemí Herrero
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige, Italy
- Present Address: Institute of Entomology, Biology Centre-The Czech Academy of Sciences, Branišovská 31/1160, České Budějovice, 37005, Czech Republic
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9000, Ghent, Belgium
| | - Luisa Lenzi
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige, Italy
| | - Alberto Pellegrini
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige, Italy
| | - Gerardo Puopolo
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige, Italy
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9000, Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, Hatfield Campus, 0028, Pretoria, South Africa
| | - Ilaria Pertot
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige, Italy
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47588
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Epithelial Coculture and l-Lactate Promote Growth of Helicobacter cinaedi under H2-Free Aerobic Conditions. Appl Environ Microbiol 2016; 82:6701-6714. [PMID: 27613684 DOI: 10.1128/aem.01943-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/01/2016] [Indexed: 11/20/2022] Open
Abstract
Helicobacter cinaedi is an emerging opportunistic pathogen associated with infections of diverse anatomic sites. Nevertheless, the species demonstrates fastidious axenic growth; it has been described as requiring a microaerobic atmosphere, along with a strong preference for supplemental H2 gas. In this context, we examined the hypothesis that in vitro growth of H. cinaedi could be enhanced by coculture with human epithelial cells. When inoculated (in Ham's F12 medium) over Caco-2 monolayers, the type strain (ATCC BAA-847) gained the ability to proliferate under H2-free aerobic conditions. Identical results were observed during coculture with several other monolayer types (LS-174T, AGS, and HeLa). Under chemically defined conditions, 40 amino acids and carboxylates were screened for their effect on the organism's atmospheric requirements. Several molecules promoted H2-free aerobic proliferation, although it occurred most prominently with millimolar concentrations of l-lactate. The growth response of H. cinaedi to Caco-2 cells and l-lactate was confirmed with a collection of 12 human-derived clinical strains. mRNA sequencing was next performed on the type strain under various growth conditions. In addition to providing a whole-transcriptome profile of H. cinaedi, this analysis demonstrated strong constitutive expression of the l-lactate utilization locus, as well as differential transcription of terminal respiratory proteins as a function of Caco-2 coculture and l-lactate supplementation. Overall, these findings challenge traditional views of H. cinaedi as an obligate microaerophile. IMPORTANCE H. cinaedi is an increasingly recognized pathogen in people with compromised immune systems. Atypical among other members of its bacterial class, H. cinaedi has been associated with infections of diverse anatomic sites. Growing H. cineadi in the laboratory is quite difficult, due in large part to the need for a specialized atmosphere. The suboptimal growth of H. cinaedi is an obstacle to clinical diagnosis, and it also limits investigation into the organism's biology. The current work shows that H. cinaedi has more flexible atmospheric requirements in the presence of host cells and a common host-derived molecule. This nutritional interplay raises new questions about how the organism behaves during human infections and provides insights for how to optimize its laboratory cultivation.
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47589
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Nguyen T, Bhatti A, Yang S, Nahavandi S. RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process. PLoS One 2016; 11:e0164766. [PMID: 27783633 PMCID: PMC5082617 DOI: 10.1371/journal.pone.0164766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/30/2016] [Indexed: 11/28/2022] Open
Abstract
This paper introduces an approach to classification of RNA-seq read counts using grey relational analysis (GRA) and Bayesian Gaussian process (GP) models. Read counts are transformed to microarray-like data to facilitate normal-based statistical methods. GRA is designed to select differentially expressed genes by integrating outcomes of five individual feature selection methods including two-sample t-test, entropy test, Bhattacharyya distance, Wilcoxon test and receiver operating characteristic curve. GRA performs as an aggregate filter method through combining advantages of the individual methods to produce significant feature subsets that are then fed into a nonparametric GP model for classification. The proposed approach is verified by using two benchmark real datasets and the five-fold cross-validation method. Experimental results show the performance dominance of the GRA-based feature selection method as well as GP classifier against their competing methods. Moreover, the results demonstrate that GRA-GP considerably dominates the sparse Poisson linear discriminant analysis classifiers, which were introduced specifically for read counts, on different number of features. The proposed approach therefore can be implemented effectively in real practice for read count data analysis, which is useful in many applications including understanding disease pathogenesis, diagnosis and treatment monitoring at the molecular level.
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Affiliation(s)
- Thanh Nguyen
- Institute for Intelligent Systems Research and Innovation, Deakin University, Victoria, Australia
- * E-mail:
| | - Asim Bhatti
- Institute for Intelligent Systems Research and Innovation, Deakin University, Victoria, Australia
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, California, United States of America
| | - Saeid Nahavandi
- Institute for Intelligent Systems Research and Innovation, Deakin University, Victoria, Australia
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47590
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Lindsay SJ, Xu Y, Lisgo SN, Harkin LF, Copp AJ, Gerrelli D, Clowry GJ, Talbot A, Keogh MJ, Coxhead J, Santibanez-Koref M, Chinnery PF. HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development. Front Neuroanat 2016; 10:86. [PMID: 27833533 PMCID: PMC5080337 DOI: 10.3389/fnana.2016.00086] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Affiliation(s)
- Susan J Lindsay
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Steven N Lisgo
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Lauren F Harkin
- Institute of Genetic Medicine, Newcastle UniversityNewcastle upon Tyne, UK; Institute of Neuroscience, Newcastle UniversityNewcastle upon Tyne, UK
| | - Andrew J Copp
- Institute of Child Health, University College London London, UK
| | - Dianne Gerrelli
- Institute of Child Health, University College London London, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University Newcastle upon Tyne, UK
| | - Aysha Talbot
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Michael J Keogh
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Jonathan Coxhead
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | | | - Patrick F Chinnery
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
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47591
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Wan ZY, Xia JH, Lin G, Wang L, Lin VCL, Yue GH. Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia. Sci Rep 2016; 6:35903. [PMID: 27782217 PMCID: PMC5080608 DOI: 10.1038/srep35903] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 10/07/2016] [Indexed: 12/19/2022] Open
Abstract
Sexual dimorphism is an interesting biological phenomenon. Previous studies showed that DNA methylation might play a role in sexual dimorphism. However, the overall picture of the genome-wide methylation landscape in sexually dimorphic species remains unclear. We analyzed the DNA methylation landscape and transcriptome in hybrid tilapia (Oreochromis spp.) using whole genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). We found 4,757 sexually dimorphic differentially methylated regions (DMRs), with significant clusters of DMRs located on chromosomal regions associated with sex determination. CpG methylation in promoter regions was negatively correlated with the gene expression level. MAPK/ERK pathway was upregulated in male tilapia. We also inferred active cis-regulatory regions (ACRs) in skeletal muscle tissues from WGBS datasets, revealing sexually dimorphic cis-regulatory regions. These results suggest that DNA methylation contribute to sex-specific phenotypes and serve as resources for further investigation to analyze the functions of these regions and their contributions towards sexual dimorphisms.
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Affiliation(s)
- Zi Yi Wan
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore.,School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, 637551 Singapore
| | - Jun Hong Xia
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore.,State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Grace Lin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore.,School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, 637551 Singapore
| | - Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore
| | - Valerie C L Lin
- School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, 637551 Singapore
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore.,School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, 637551 Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive, 117543 Singapore
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47592
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Wu C, Li X, Guo S, Wong SM. Analyses of RNA-Seq and sRNA-Seq data reveal a complex network of anti-viral defense in TCV-infected Arabidopsis thaliana. Sci Rep 2016; 6:36007. [PMID: 27782158 PMCID: PMC5080594 DOI: 10.1038/srep36007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/10/2016] [Indexed: 01/01/2023] Open
Abstract
In order to identify specific plant anti-viral genes related to the miRNA regulatory pathway, RNA-Seq and sRNA-Seq were performed using Arabidopsis WT and dcl1-9 mutant line. A total of 5,204 DEGs were identified in TCV-infected WT plants. In contrast, only 595 DEGs were obtained in the infected dcl1-9 mutant plants. GO enrichment analysis of the shared DEGs and dcl1-9 unique DEGs showed that a wide range of biological processes were affected in the infected WT plants. In addition, miRNAs displayed different patterns between mock and infected WT plants. This is the first global view of dcl1-9 transcriptome which provides TCV responsive miRNAs data. In conclusion, our results indicated the significance of DCL1 and suggested that PPR genes may play an important role in plant anti-viral defense.
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Affiliation(s)
- Chao Wu
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Xinyue Li
- Vishuo Biomedical Pte Ltd, Science Park II, Singapore
| | - Song Guo
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sek-Man Wong
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- Temasek Life Sciences Laboratory, Singapore
- National University of Singapore Suzhou Research Institute, Suzhou Industrial Park, Jiangsu, China
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47593
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Al Mahi N, Begum M. A two-step integrated approach to detect differentially expressed genes in RNA-Seq data. J Bioinform Comput Biol 2016; 14:1650034. [PMID: 27774870 DOI: 10.1142/s0219720016500347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
One of the primary objectives of ribonucleic acid (RNA) sequencing or RNA-Seq experiment is to identify differentially expressed (DE) genes in two or more treatment conditions. It is a common practice to assume that all read counts from RNA-Seq data follow overdispersed (OD) Poisson or negative binomial (NB) distribution, which is sometimes misleading because within each condition, some genes may have unvarying transcription levels with no overdispersion. In such a case, it is more appropriate and logical to consider two sets of genes: OD and non-overdispersed (NOD). We propose a new two-step integrated approach to distinguish DE genes in RNA-Seq data using standard Poisson and NB models for NOD and OD genes, respectively. This is an integrated approach because this method can be merged with any other NB-based methods for detecting DE genes. We design a simulation study and analyze two real RNA-Seq data to evaluate the proposed strategy. We compare the performance of this new method combined with the three [Formula: see text]-software packages namely edgeR, DESeq2, and DSS with their default settings. For both the simulated and real data sets, integrated approaches perform better or at least equally well compared to the regular methods embedded in these [Formula: see text]-packages.
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Affiliation(s)
- Naim Al Mahi
- * Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Munni Begum
- † Department of Mathematical Sciences, Ball State University, Muncie, IN 47306, USA
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47594
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Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. Nat Commun 2016; 7:13197. [PMID: 28959951 PMCID: PMC5093340 DOI: 10.1038/ncomms13197] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 09/11/2016] [Indexed: 02/06/2023] Open
Abstract
Thousands of long non-coding RNAs (lncRNAs) lie interspersed with coding genes across the genome, and a small subset has been implicated as downstream effectors in oncogenic pathways. Here we make use of transcriptome and exome sequencing data from thousands of tumours across 19 cancer types, to identify lncRNAs that are induced or repressed in relation to somatic mutations in key oncogenic driver genes. Our screen confirms known coding and non-coding effectors and also associates many new lncRNAs to relevant pathways. The associations are often highly reproducible across cancer types, and while many lncRNAs are co-expressed with their protein-coding hosts or neighbours, some are intergenic and independent. We highlight lncRNAs with possible functions downstream of the tumour suppressor TP53 and the master antioxidant transcription factor NFE2L2. Our study provides a comprehensive overview of lncRNA transcriptional alterations in relation to key driver mutational events in human cancers.
Long non-coding RNAs are implicated in multiple aspects of tumourigenesis. Here, the authors generate a landscape of these macromolecules in a wide array of cancer types and examine which RNAs are transcriptionally altered in relation to somatic driver mutations in established coding cancer genes.
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47595
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Tran VDT, Souiai O, Romero-Barrios N, Crespi M, Gautheret D. Detection of generic differential RNA processing events from RNA-seq data. RNA Biol 2016; 13:59-67. [PMID: 26849165 DOI: 10.1080/15476286.2015.1118604] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
RNA-seq data analysis has revealed abundant alternative splicing in eukaryotic mRNAs. However, splicing is only one of many processing events that transcripts may undergo during their lifetime. We present here RNAprof (RNA profile analysis), a program for the detection of differential processing events from the comparison of RNA-seq experiments. RNAprof implements a specific gene-level normalization procedure and compares RNA-seq coverage profiles at nucleotide resolution to detect regions of significant coverage differences, independently of splice sites or other gene features. We used RNAprof to analyze the effect of alternative-splicing regulators NSRa and NSRb on the Arabidopsis thaliana transcriptome. A number of intron retention events and alternative transcript structures were specifically detected by RNAprof and confirmed by qRT-PCR. Further tests using a public Mus musculus RNA-seq dataset and comparisons with other RNA isoform predictors showed that RNAprof uniquely identified sets of highly significant processing events as well as other relevant library-specific differences in RNA-seq profiles. This highlights an important layer of variation that remains undetected by current protocols for RNA-seq analysis.
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Affiliation(s)
- Van Du T Tran
- a I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud , 1 avenue de la terrasse, 91198 Gif sur Yvette , France.,b Swiss Institute of Bioinformatics, Quartier Sorge , bâtiment Génopode - 1015 Lausanne , Switzerland
| | - Oussema Souiai
- a I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud , 1 avenue de la terrasse, 91198 Gif sur Yvette , France
| | - Natali Romero-Barrios
- c Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité , Bâtiment 630, 91405 Orsay , France
| | - Martin Crespi
- c Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité , Bâtiment 630, 91405 Orsay , France
| | - Daniel Gautheret
- a I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud , 1 avenue de la terrasse, 91198 Gif sur Yvette , France
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47596
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Lloret-Llinares M, Mapendano CK, Martlev LH, Lykke-Andersen S, Jensen TH. Relationships between PROMPT and gene expression. RNA Biol 2016; 13:6-14. [PMID: 26574648 DOI: 10.1080/15476286.2015.1109769] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Most mammalian protein-coding gene promoters are divergent, yielding promoter upstream transcripts (PROMPTs) in the reverse direction from their conventionally produced mRNAs. PROMPTs are rapidly degraded by the RNA exosome rendering a general function of these molecules elusive. Yet, levels of certain PROMPTs are altered in stress conditions, like the DNA damage response (DDR), suggesting a possible regulatory role for at least a subset of these molecules. Here we manipulate PROMPT levels by either exosome depletion or UV treatment and analyze possible effects on their neighboring genes. For the CTSZ and DAP genes we find that TFIIB and TBP promoter binding decrease when PROMPTs accumulate. Moreover, DNA methylation increases concomitant with the recruitment of the DNA methyltransferase DNMT3B. Thus, although a correlation between increased PROMPT levels and decreased gene activity is generally absent, some promoters may have co-opted their divergent transcript production for regulatory purposes.
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Affiliation(s)
- Marta Lloret-Llinares
- a Centre for mRNP Biogenesis and Metabolism , Department of Molecular Biology and Genetics, Aarhus University , DK-8000 , Aarhus , Denmark.,d Shared first authorship
| | - Christophe K Mapendano
- a Centre for mRNP Biogenesis and Metabolism , Department of Molecular Biology and Genetics, Aarhus University , DK-8000 , Aarhus , Denmark.,b Present address; Emergency Department , Horsens Hospital , DK-8700 Horsens , Denmark.,d Shared first authorship
| | - Lasse H Martlev
- a Centre for mRNP Biogenesis and Metabolism , Department of Molecular Biology and Genetics, Aarhus University , DK-8000 , Aarhus , Denmark.,c Present address: Seahorse Bioscience , Symbion , DK-2100 , Copenhagen , Denmark
| | - Søren Lykke-Andersen
- a Centre for mRNP Biogenesis and Metabolism , Department of Molecular Biology and Genetics, Aarhus University , DK-8000 , Aarhus , Denmark
| | - Torben Heick Jensen
- a Centre for mRNP Biogenesis and Metabolism , Department of Molecular Biology and Genetics, Aarhus University , DK-8000 , Aarhus , Denmark
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47597
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Potent and selective bivalent inhibitors of BET bromodomains. Nat Chem Biol 2016; 12:1097-1104. [PMID: 27775716 DOI: 10.1038/nchembio.2210] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 09/02/2016] [Indexed: 01/02/2023]
Abstract
Proteins of the bromodomain and extraterminal (BET) family, in particular bromodomain-containing protein 4 (BRD4), are of great interest as biological targets. BET proteins contain two separate bromodomains, and existing inhibitors bind to them monovalently. Here we describe the discovery and characterization of probe compound biBET, capable of engaging both bromodomains simultaneously in a bivalent, in cis binding mode. The evidence provided here was obtained in a variety of biophysical and cellular experiments. The bivalent binding results in very high cellular potency for BRD4 binding and pharmacological responses such as disruption of BRD4-mediator complex subunit 1 foci with an EC50 of 100 pM. These compounds will be of considerable utility as BET/BRD4 chemical probes. This work illustrates a novel concept in ligand design-simultaneous targeting of two separate domains with a drug-like small molecule-providing precedent for a potentially more effective paradigm for developing ligands for other multi-domain proteins.
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47598
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Mahajan N, Wu HJ, Bennett RL, Troche C, Licht JD, Weber JD, Maggi LB, Tomasson MH. Sabotaging of the oxidative stress response by an oncogenic noncoding RNA. FASEB J 2016; 31:482-490. [PMID: 28148777 DOI: 10.1096/fj.201600654r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/04/2016] [Indexed: 12/27/2022]
Abstract
Overexpression of the multiple myeloma set domain (MMSET) Wolf-Hirschhorn syndrome candidate 1 gene, which contains an orphan box H/ACA class small nucleolar RNA, ACA11, in an intron, is associated with several cancer types, including multiple myeloma (MM). ACA11 and MMSET are overexpressed cotranscriptionally as a result of the t(4;14) chromosomal translocation in a subset of patients with MM. RNA sequencing of CD138+ tumor cells from t(4;14)-positive and -negative MM patient bone marrow samples revealed an enhanced oxidative phosphorylation mRNA signature. Supporting these data, ACA11 overexpression in a t(4;14)-negative MM cell line, MM1.S, demonstrated enhanced reactive oxygen species (ROS) levels. In addition, an enhancement of cell proliferation, increased soft agar colony size, and elevated ERK1/2 phosphorylation were observed. This ACA11-driven hyperproliferative phenotype depended on increased ROS levels as exogenously added antioxidants attenuate the increased proliferation. A major transcriptional regulator of the cellular antioxidant response, nuclear factor (erythroid-derived 2)-like 2 (NRF2), shuttled to the nucleus, as expected, in response to ACA11-driven increases in ROS; however, transcriptional up-regulation of some of NRF2's antioxidant target genes was abrogated in the presence of ACA11 overexpression. These data show for the first time that ACA11 promotes proliferation through inhibition of NRF2 function resulting in sustained ROS levels driving cancer cell proliferation.-Mahajan, N., Wu, H.-J., Bennett, R. L., Troche, C., Licht, J. D., Weber, J. D., Maggi, L. B., Jr., Tomasson, M. H. Sabotaging of the oxidative stress response by an oncogenic noncoding RNA.
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Affiliation(s)
- Nitin Mahajan
- Division of Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Hua-Jun Wu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; and
| | - Richard L Bennett
- Division of Hematology and Oncology, Department of Medicine, University of Florida Health Cancer Center, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Catalina Troche
- Division of Hematology and Oncology, Department of Medicine, University of Florida Health Cancer Center, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jonathan D Licht
- Division of Hematology and Oncology, Department of Medicine, University of Florida Health Cancer Center, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jason D Weber
- Division of Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Leonard B Maggi
- Division of Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Michael H Tomasson
- Division of Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA;
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47599
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Bayin NS, Frenster JD, Kane JR, Rubenstein J, Modrek AS, Baitalmal R, Dolgalev I, Rudzenski K, Scarabottolo L, Crespi D, Redaelli L, Snuderl M, Golfinos JG, Doyle W, Pacione D, Parker EC, Chi AS, Heguy A, MacNeil DJ, Shohdy N, Zagzag D, Placantonakis DG. GPR133 (ADGRD1), an adhesion G-protein-coupled receptor, is necessary for glioblastoma growth. Oncogenesis 2016; 5:e263. [PMID: 27775701 PMCID: PMC5117849 DOI: 10.1038/oncsis.2016.63] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/09/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma (GBM) is a deadly primary brain malignancy with extensive intratumoral hypoxia. Hypoxic regions of GBM contain stem-like cells and are associated with tumor growth and angiogenesis. The molecular mechanisms that regulate tumor growth in hypoxic conditions are incompletely understood. Here, we use primary human tumor biospecimens and cultures to identify GPR133 (ADGRD1), an orphan member of the adhesion family of G-protein-coupled receptors, as a critical regulator of the response to hypoxia and tumor growth in GBM. GPR133 is selectively expressed in CD133+ GBM stem cells (GSCs) and within the hypoxic areas of PPN in human biospecimens. GPR133 mRNA is transcriptionally upregulated by hypoxia in hypoxia-inducible factor 1α (Hif1α)-dependent manner. Genetic inhibition of GPR133 with short hairpin RNA reduces the prevalence of CD133+ GSCs, tumor cell proliferation and tumorsphere formation in vitro. Forskolin rescues the GPR133 knockdown phenotype, suggesting that GPR133 signaling is mediated by cAMP. Implantation of GBM cells with short hairpin RNA-mediated knockdown of GPR133 in the mouse brain markedly reduces tumor xenograft formation and increases host survival. Analysis of the TCGA data shows that GPR133 expression levels are inversely correlated with patient survival. These findings indicate that GPR133 is an important mediator of the hypoxic response in GBM and has significant protumorigenic functions. We propose that GPR133 represents a novel molecular target in GBM and possibly other malignancies where hypoxia is fundamental to pathogenesis.
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Affiliation(s)
- N S Bayin
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
- Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, NY, USA
| | - J D Frenster
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
- Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, NY, USA
| | - J R Kane
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
| | - J Rubenstein
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
| | - A S Modrek
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
| | - R Baitalmal
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - I Dolgalev
- Genome Technology Center, New York University School of Medicine, New York, NY, USA
| | - K Rudzenski
- Office for Therapeutic Alliances, New York University School of Medicine, New York, NY, USA
| | | | | | | | - M Snuderl
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Brain Tumor Center, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - J G Golfinos
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
- Brain Tumor Center, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - W Doyle
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
| | - D Pacione
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
| | - E C Parker
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
| | - A S Chi
- Brain Tumor Center, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - A Heguy
- Genome Technology Center, New York University School of Medicine, New York, NY, USA
| | - D J MacNeil
- Office for Therapeutic Alliances, New York University School of Medicine, New York, NY, USA
| | - N Shohdy
- Office for Therapeutic Alliances, New York University School of Medicine, New York, NY, USA
| | - D Zagzag
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Brain Tumor Center, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - D G Placantonakis
- Department of Neurosurgery, New York University School of Medicine, New York, NY, USA
- Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, NY, USA
- Brain Tumor Center, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
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47600
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Impey S, Jopson T, Pelz C, Tafessu A, Fareh F, Zuloaga D, Marzulla T, Riparip LK, Stewart B, Rosi S, Turker MS, Raber J. Short- and long-term effects of 56Fe irradiation on cognition and hippocampal DNA methylation and gene expression. BMC Genomics 2016; 17:825. [PMID: 27776477 PMCID: PMC5078898 DOI: 10.1186/s12864-016-3110-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 09/22/2016] [Indexed: 12/21/2022] Open
Abstract
Background Astronauts are exposed to 56Fe ions that may pose a significant health hazard during and following prolonged missions in deep space. We showed previously that object recognition requiring the hippocampus, a structure critical for cognitive function, is affected in 2-month-old mice irradiated with 56Fe ions. Here we examined object recognition in 6-month-old mice irradiated with 56Fe ions, a biological age more relevant to the typical ages of astronauts. Moreover, because the mechanisms mediating the detrimental effects of 56Fe ions on hippocampal function are unclear, we examined changes in hippocampal networks involved in synaptic plasticity and memory, gene expression, and epigenetic changes in cytosine methylation (5mC) and hydroxymethylation (5hmC) that could accompany changes in gene expression. We assessed the effects of whole body 56Fe ion irradiation at early (2 weeks) and late (20 weeks) time points on hippocampus-dependent memory and hippocampal network stability, and whether these effects are associated with epigenetic changes in hippocampal DNA methylation (both 5mC and 5hmC) and gene expression. Results At the two-week time point, object recognition and network stability were impaired following irradiation at the 0.1 and 0.4 Gy dose, but not following irradiation at the 0.2 Gy dose. No impairments in object recognition or network stability were seen at the 20-week time point at any irradiation dose used. Consistent with this pattern, the significance of pathways for gene categories for 5hmC was lower, though not eliminated, at the 20-week time point compared to the 2-week time point. Similarly, significant changes were observed for 5mC gene pathways at the 2-week time point, but no significant gene categories were observed at the 20-week time point. Only the 5hmC changes tracked with gene expression changes. Conclusions Dose- and time-dependent epigenomic remodeling in the hippocampus following 56Fe ion exposure correlates with behavioral changes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3110-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Soren Impey
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA. .,Department of Cell, Developmental Biology, and Cancer Biology, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Timothy Jopson
- Brain and Spinal Injury Center, University of California, San Francisco, San Francisco, CA, 94110, USA.,Departments of Physical Therapy Rehabilitation Science, University of California, San Francisco, San Francisco, CA, 94110, USA.,Neurological Surgery, University of California San Francisco, Zuckerberg San Francisco General Hospital, San Francisco, CA, 94110, USA
| | - Carl Pelz
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Amanuel Tafessu
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Fatema Fareh
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Damian Zuloaga
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Tessa Marzulla
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Lara-Kirstie Riparip
- Brain and Spinal Injury Center, University of California, San Francisco, San Francisco, CA, 94110, USA.,Departments of Physical Therapy Rehabilitation Science, University of California, San Francisco, San Francisco, CA, 94110, USA.,Neurological Surgery, University of California San Francisco, Zuckerberg San Francisco General Hospital, San Francisco, CA, 94110, USA
| | - Blair Stewart
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Susanna Rosi
- Brain and Spinal Injury Center, University of California, San Francisco, San Francisco, CA, 94110, USA.,Departments of Physical Therapy Rehabilitation Science, University of California, San Francisco, San Francisco, CA, 94110, USA.,Neurological Surgery, University of California San Francisco, Zuckerberg San Francisco General Hospital, San Francisco, CA, 94110, USA
| | - Mitchell S Turker
- Oregon Institute of Occupational Health Sciences and Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA. .,Departments of Neurology and Radiation Medicine, Oregon Health and Science University, Portland, OR, 97239, USA. .,Division of Neuroscience ONPRC, Oregon Health and Science University, Portland, OR, 97239, USA.
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