1
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Karczewski KJ, Solomonson M, Chao KR, Goodrich JK, Tiao G, Lu W, Riley-Gillis BM, Tsai EA, Kim HI, Zheng X, Rahimov F, Esmaeeli S, Grundstad AJ, Reppell M, Waring J, Jacob H, Sexton D, Bronson PG, Chen X, Hu X, Goldstein JI, King D, Vittal C, Poterba T, Palmer DS, Churchhouse C, Howrigan DP, Zhou W, Watts NA, Nguyen K, Nguyen H, Mason C, Farnham C, Tolonen C, Gauthier LD, Gupta N, MacArthur DG, Rehm HL, Seed C, Philippakis AA, Daly MJ, Davis JW, Runz H, Miller MR, Neale BM. Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes. Cell Genom 2022; 2:100168. [PMID: 36778668 PMCID: PMC9903662 DOI: 10.1016/j.xgen.2022.100168] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 07/16/2022] [Indexed: 01/20/2023]
Abstract
Genome-wide association studies have successfully discovered thousands of common variants associated with human diseases and traits, but the landscape of rare variations in human disease has not been explored at scale. Exome-sequencing studies of population biobanks provide an opportunity to systematically evaluate the impact of rare coding variations across a wide range of phenotypes to discover genes and allelic series relevant to human health and disease. Here, we present results from systematic association analyses of 4,529 phenotypes using single-variant and gene tests of 394,841 individuals in the UK Biobank with exome-sequence data. We find that the discovery of genetic associations is tightly linked to frequency and is correlated with metrics of deleteriousness and natural selection. We highlight biological findings elucidated by these data and release the dataset as a public resource alongside the Genebass browser for rapidly exploring rare-variant association results.
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Affiliation(s)
- Konrad J. Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia K. Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wenhan Lu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Hye In Kim
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xiuwen Zheng
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Fedik Rahimov
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Sahar Esmaeeli
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Mark Reppell
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Jeff Waring
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Howard Jacob
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | | | - Xing Chen
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xinli Hu
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Jacqueline I. Goldstein
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel King
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Vittal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Duncan S. Palmer
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claire Churchhouse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel P. Howrigan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas A. Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Huy Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cara Mason
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Farnham
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Charlotte Tolonen
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Laura D. Gauthier
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Namrata Gupta
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cotton Seed
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - J. Wade Davis
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Melissa R. Miller
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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2
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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3
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Zheng X, Davis JW. SAIGEgds-an efficient statistical tool for large-scale PheWAS with mixed models. Bioinformatics 2021; 37:728-730. [PMID: 32898220 DOI: 10.1093/bioinformatics/btaa731] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/16/2020] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Phenome-wide association studies (PheWASs) are known to be a powerful tool in discovery and replication of genetic association studies. To reduce the computational burden of PheWAS in the large cohorts, such as the UK Biobank, the SAIGE method has been proposed to control for case-control imbalance and sample relatedness in a tractable manner. However, SAIGE is still computationally intensive when deployed in analyzing the associations of thousands of ICD10-coded phenotypes with whole-genome imputed genotype data. Here, we present a new high-performance statistical R package (SAIGEgds) for large-scale PheWAS using generalized linear mixed models. The package implements the SAIGE method in optimized C++ codes, taking advantage of sparse genotype dosages and integrating the efficient genomic data structure file format. Benchmarks using the UK Biobank White British genotype data (N ≈ 430 K) with coronary heart disease and simulated cases show that the implementation in SAIGEgds is 5-6 times faster than the SAIGE R package. When used in conjunction with high-performance computing clusters, SAIGEgds provides an efficient analysis pipeline for biobank-scale PheWAS. AVAILABILITY AND IMPLEMENTATION https://bioconductor.org/packages/SAIGEgds; vignettes included. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiuwen Zheng
- Genomics Research Center, AbbVie Inc., North Chicago, IL 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc., North Chicago, IL 60064, USA
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4
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Kosmicki JA, Horowitz JE, Banerjee N, Lanche R, Marcketta A, Maxwell E, Bai X, Sun D, Backman JD, Sharma D, Kang HM, O'Dushlaine C, Yadav A, Mansfield AJ, Li AH, Watanabe K, Gurski L, McCarthy SE, Locke AE, Khalid S, O'Keeffe S, Mbatchou J, Chazara O, Huang Y, Kvikstad E, O'Neill A, Nioi P, Parker MM, Petrovski S, Runz H, Szustakowski JD, Wang Q, Wong E, Cordova-Palomera A, Smith EN, Szalma S, Zheng X, Esmaeeli S, Davis JW, Lai YP, Chen X, Justice AE, Leader JB, Mirshahi T, Carey DJ, Verma A, Sirugo G, Ritchie MD, Rader DJ, Povysil G, Goldstein DB, Kiryluk K, Pairo-Castineira E, Rawlik K, Pasko D, Walker S, Meynert A, Kousathanas A, Moutsianas L, Tenesa A, Caulfield M, Scott R, Wilson JF, Baillie JK, Butler-Laporte G, Nakanishi T, Lathrop M, Richards JB, Jones M, Balasubramanian S, Salerno W, Shuldiner AR, Marchini J, Overton JD, Habegger L, Cantor MN, Reid JG, Baras A, Abecasis GR, Ferreira MA. A catalog of associations between rare coding variants and COVID-19 outcomes. medRxiv 2021:2020.10.28.20221804. [PMID: 33655273 PMCID: PMC7924298 DOI: 10.1101/2020.10.28.20221804] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.
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Affiliation(s)
- J A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J E Horowitz
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - N Banerjee
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - R Lanche
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Marcketta
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - E Maxwell
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - X Bai
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sun
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sharma
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - H M Kang
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - C O'Dushlaine
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Yadav
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A J Mansfield
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A H Li
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K Watanabe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Gurski
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S E McCarthy
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A E Locke
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Khalid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S O'Keeffe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Mbatchou
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - O Chazara
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Y Huang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - E Kvikstad
- Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, NJ 08543, USA
| | - A O'Neill
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - P Nioi
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - M M Parker
- Alnylam Pharmaceuticals, 675 West Kendall St, Cambridge, MA 02142, USA
| | - S Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - H Runz
- Biogen, 300 Binney St, Cambridge, MA 02142, USA
| | - J D Szustakowski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Q Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - E Wong
- Biogen, 300 Binney St, Cambridge, MA 02142, USA
| | | | - E N Smith
- Takeda California Inc., 9625 Towne Centre Dr, San Diego, CA 92121, USA
| | - S Szalma
- Takeda California Inc., 9625 Towne Centre Dr, San Diego, CA 92121, USA
| | - X Zheng
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - S Esmaeeli
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - J W Davis
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - Y-P Lai
- Pfizer, Inc., 1 Portland Street, Cambridge MA 02139, USA
| | - X Chen
- Pfizer, Inc., 1 Portland Street, Cambridge MA 02139, USA
| | | | | | | | | | - A Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Sirugo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - D J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - D B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics & Development, Columbia University, New York, NY 10032, USA
| | - K Kiryluk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - E Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - K Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - D Pasko
- Genomics England, London EC1M 6BQ, UK
| | - S Walker
- Genomics England, London EC1M 6BQ, UK
| | - A Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | | | | | - A Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - M Caulfield
- Genomics England, London EC1M 6BQ, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - R Scott
- Genomics England, London EC1M 6BQ, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - J F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - J K Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK
| | - G Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec H3A 0G4, Canada
| | - T Nakanishi
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Research Fellow, Japan Society for the Promotion of Science
| | - M Lathrop
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec H3A 0G4, Canada
| | - J B Richards
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec H3A 0G4, Canada
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Department of Twins Research, King's College London, London WC2R 2LS, UK
| | - M Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Balasubramanian
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - W Salerno
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A R Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Marchini
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Overton
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Habegger
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M N Cantor
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J G Reid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - G R Abecasis
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M A Ferreira
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
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5
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Abstract
Abstract
Casestudy: The utilization of checkpoint inhibitors such as programmed cell death protein 1 (PD-1/PD-L1) inhibitors (nivolumab) and cytotoxic T-lymphocyte antigen 4 inhibitors (ipilimumab) for treatment of certain malignancies has steadily gained popularity. Medication related colitis is uncommon, with a reported incidence of 1–9% depending on the checkpoint inhibitor used, and the histologic features have been characterized in recent literature. Because of the immunomodulating effect of these drugs, infectious colitis is in the differential diagnosis of enteritis. Multi-drug therapy in many of these patients further complicates identification of the culprit drug. We present the case of a 63-year-old male with metastatic renal cell carcinoma being treated with both nivolumab and ipilimumab who presented with acute on chronic non-bloody diarrhea. His clinical course was complicated by hypotension, acidosis and coagulopathy. The clinical differential for his colitis was cytomegalovirus infection versus a checkpoint inhibitor colitis. Colonoscopy revealed continuous circumferential loss of vascularity and diffuse erythema throughout the colon. Histology showed acute colitis with prominent apoptosis, cryptitis, crypt abscesses, and rare ringed mitotic figures, but without architectural distortion. Occasional smooth purple crystals consistent with pill material were present in the mucosa, but without significant tissue reaction. No pathogenic organisms were identified, and a cytomegalovirus immunostain was negative. These histologic findings in concert with the clinical history are consistent with checkpoint inhibitor colitis and multi-drug effect. A review of the patient’s chart showed cholestyramine was added to the patient’s regimen during hospitalization, which was consistent with the morphologic appearance of the crystals. Given the acute complications of checkpoint inhibitor induced enterocolitis and potential for increased morbidity (rare cases of bowel perforation and subsequent resection), accurate diagnosis is imperative. Management of checkpoint inhibitor associated colitis ranges from initiation of immunosuppression to checkpoint inhibitor cessation. When these findings are masked by multi-drug effect, accurate diagnosis can be difficult.
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Affiliation(s)
- J W Davis
- Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland, UNITED STATES
| | - M Canevari
- Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland, UNITED STATES
| | - J C Shaw
- Department of Pathology, Joint Pathology Center, Silver Spring, Maryland, UNITED STATES
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6
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King EA, Davis JW, Degner JF. Are drug targets with genetic support twice as likely to be approved? Revised estimates of the impact of genetic support for drug mechanisms on the probability of drug approval. PLoS Genet 2019; 15:e1008489. [PMID: 31830040 PMCID: PMC6907751 DOI: 10.1371/journal.pgen.1008489] [Citation(s) in RCA: 260] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/23/2019] [Indexed: 11/19/2022] Open
Abstract
Despite strong vetting for disease activity, only 10% of candidate new molecular entities in early stage clinical trials are eventually approved. Analyzing historical pipeline data, Nelson et al. 2015 (Nat. Genet.) concluded pipeline drug targets with human genetic evidence of disease association are twice as likely to lead to approved drugs. Taking advantage of recent clinical development advances and rapid growth in GWAS datasets, we extend the original work using updated data, test whether genetic evidence predicts future successes and introduce statistical models adjusting for target and indication-level properties. Our work confirms drugs with genetically supported targets were more likely to be successful in Phases II and III. When causal genes are clear (Mendelian traits and GWAS associations linked to coding variants), we find the use of human genetic evidence increases approval by greater than two-fold, and, for Mendelian associations, the positive association holds prospectively. Our findings suggest investments into genomics and genetics are likely to be beneficial to companies deploying this strategy. The growth of human genetics resources has the potential to help us develop better drugs. By looking at whether and how historical drug approvals could have been predicted from our current knowledge of human genetics, we can validate this approach and assess which types of genetic evidence are most likely to be useful in guiding drug discovery. Validation is important because we are often uncertain about the biological mechanisms behind genetic variants linked to disease. Most associated variants do not occur within protein-coding regions of the genome, and it is difficult to tell which of many nearby genes is contributing to disease risk. In this paper, we confirm previous correlations between genetic evidence and historical drug approvals. We find genetic evidence from severe genetic disorders and from genetic variants that alter protein sequence is more strongly associated with historical approvals. We offer statistical approaches for prioritizing new drug candidates based on whether their mechanisms are supported by human genetic evidence.
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Affiliation(s)
- Emily A. King
- Department of Computational Genomics, AbbVie, North Chicago, Illinois, United States of America
- * E-mail:
| | - J. Wade Davis
- Department of Computational Genomics, AbbVie, North Chicago, Illinois, United States of America
| | - Jacob F. Degner
- Department of Computational Genomics, AbbVie, North Chicago, Illinois, United States of America
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7
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Brown SM, Meuth AI, Davis JW, Rector RS, Bender SB. Mineralocorticoid receptor antagonism reverses diabetes-related coronary vasodilator dysfunction: A unique vascular transcriptomic signature. Pharmacol Res 2018; 134:100-108. [PMID: 29870805 DOI: 10.1016/j.phrs.2018.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 01/09/2023]
Abstract
Coronary microvascular dysfunction predicts and may be a proximate cause of cardiac dysfunction and mortality in diabetes; however, few effective treatments exist for these conditions. We recently demonstrated that mineralocorticoid receptor (MR) antagonism reversed cardiovascular dysfunction in early-stage obesity/insulin resistance. The mechanisms underlying this benefit of MR antagonism and its relevance in the setting of long-term obesity complications like diabetes; however, remain unclear. Thus, the present study evaluated the impact of MR antagonism on diabetes-related coronary dysfunction and defines the MR-dependent vascular transcriptome in the Otsuka Long-Evans Tokushima Fatty (OLETF) rat recapitulating later stages of human diabetes. OLETF rats were treated with spironolactone (Sp) and compared to untreated OLETF and lean Long-Evans Tokushima Otsuka rats. Sp treatment attenuated diabetes-associated adipose and cardiac inflammation/fibrosis and improved coronary endothelium-dependent vasodilation but did not alter enhanced coronary vasoconstriction, blood pressure, or metabolic parameters in OLETF rats. Further mechanistic studies using RNA deep sequencing of OLETF rat aortas revealed 157 differentially expressed genes following Sp including upregulation of genes involved in the molecular regulation of nitric oxide bioavailability (Hsp90ab1, Ahsa1, Ahsa2) as well as novel changes in α1D adrenergic receptors (Adra1d), cyclooxygenase-2 (Ptgs2), and modulatory factors of these pathways (Ackr3, Acsl4). Further, Ingenuity Pathway Analysis predicted inhibition of upstream inflammatory regulators by Sp and inhibition of 'migration of endothelial cells', 'differentiation of smooth muscle', and 'angiogenesis' biological functions by Sp in diabetes. Thus, this study is the first to define the MR-dependent vascular transcriptome underlying treatment of diabetes-related coronary microvascular dysfunction by Sp.
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Affiliation(s)
- Scott M Brown
- Research Service, Harry S Truman Memorial Veterans Hospital, Columbia, MO, USA; Biomedical Sciences, University of Missouri, Columbia, MO, USA
| | - Alex I Meuth
- Research Service, Harry S Truman Memorial Veterans Hospital, Columbia, MO, USA; Biomedical Sciences, University of Missouri, Columbia, MO, USA
| | - J Wade Davis
- MU Informatics Institute, University of Missouri, Columbia, MO, USA; Health Management and Informatics, University of Missouri, Columbia, MO, USA; Statistics, University of Missouri, Columbia, MO, USA
| | - R Scott Rector
- Research Service, Harry S Truman Memorial Veterans Hospital, Columbia, MO, USA; Nutrition and Exercise Physiology, University of Missouri, Columbia, MO, USA; Medicine-Division of Gastroenterology and Hepatology, University of Missouri, School of Medicine, Columbia, MO, USA
| | - Shawn B Bender
- Research Service, Harry S Truman Memorial Veterans Hospital, Columbia, MO, USA; Biomedical Sciences, University of Missouri, Columbia, MO, USA; Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA.
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8
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Waring JF, Davis JW, Dumas E, Cohen D, Idler K, Abel S, Georgantas R, Podsadecki T, Dutta S. Epigenetic analysis of the IFNλ3 gene identifies a novel marker for response to therapy in HCV-infected subjects. J Viral Hepat 2017; 24:397-403. [PMID: 27925355 DOI: 10.1111/jvh.12661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/22/2016] [Indexed: 12/31/2022]
Abstract
Chronic hepatitis C virus (HCV) infection is characterized by high interindividual variability in response to pegylated interferon and ribavirin. A genetic polymorphism on chromosome 19 (rs12979860) upstream of interferon-λ3 (IFNλ3) is associated with a twofold change in sustained virologic response rate after 48 weeks of treatment with pegylated interferon/ribavirin in HCV genotype 1 (GT1) treatment-naïve patients. We conducted epigenetic analysis on the IFNλ3 promoter to investigate whether DNA methylation is associated with response to HCV therapy. DNA samples from HCV GT1-infected subjects receiving an interferon-free paritaprevir-containing combination regimen (N=540) and from HCV-uninfected, healthy controls (N=124) were analysed for IFNλ3 methylation levels. Methylation was strongly associated with rs12979860 allele status whether adjusting for HCV status (r=65.0%, 95% CI: [60.2%, 69.5%]), or not (r=64.4%), both with P<2.2×10-16 . In HCV GT1-infected subjects, C/C genotypes had significantly lower methylation levels relative to C/T or T/T genotypes (P<1×10-14 ), with each T allele resulting in a nine-unit increase in mean methylation level. Methylation levels did not correlate with response in subjects treated for 12 or 24 weeks. However, non-C/C subjects with higher methylation levels were more likely to relapse when treatment duration was 8 weeks. This analysis suggests that methylation status of the IFNλ3 promoter region may be a useful parameter that identifies patients more likely to relapse following HCV therapy; however, continuing therapy for a sufficient duration can overcome this difference. These findings may provide mechanistic insight into the role of IFNλ3 genetic variants in HCV treatment response.
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Affiliation(s)
| | | | - E Dumas
- AbbVie Inc., North Chicago, IL, USA
| | - D Cohen
- AbbVie Inc., North Chicago, IL, USA
| | - K Idler
- AbbVie Inc., North Chicago, IL, USA
| | - S Abel
- AbbVie Inc., North Chicago, IL, USA
| | | | | | - S Dutta
- AbbVie Inc., North Chicago, IL, USA
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9
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Blount JL, Roberts PM, Toews MD, Gardner WA, Buntin GD, Davis JW, All JN. Seasonal Population Dynamics of Megacopta cribraria (Hemiptera: Plataspidae) in Kudzu and Soybean, and Implication for Insecticidal Management in Soybean. J Econ Entomol 2017; 110:157-167. [PMID: 28039424 DOI: 10.1093/jee/tow281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Megacopta cribraria (F.), an invasive species introduced from Asia in 2009, is now prolific in the southeastern United States. Megacopta cribraria develops primarily on kudzu and soybean completing two generations. It is not well understood how this economic pest is affected by changes in geographic distribution in the United States or how population levels have changed since its establishment. The effect of insecticide application timing on field populations of M. cribraria is not well documented. These studies seek to understand how population dynamics of M. cribraria vary with geographic regions in Georgia. Effect of application timing on populations throughout the growing season was also examined. Weekly from 2012 to 2013, all life stages were enumerated from kudzu and soybean environments at several locations throughout Georgia from sweeps samples and flight intercept captures. Coordinates were recorded for locations, and classified as belonging to the Piedmont or Coastal Plain region of the state. Single spray trials were conducted from 2011-2014, and applications were made to soybean at intervals throughout the season. From 2012 to 2015, two kudzu patches near Griffin, GA, were monitored to detect population changes. Differences in population dynamics from locations around the state were found, but no clear effect of latitude, longitude, or region was observed. Insecticide applications applied in July suppressed nymph populations significantly better than treatments made earlier or later. Megacopta cribraria populations declined in 2014 and 2015 compared with 2012 and 2013. These studies provide the critical information for M. cribraria management in soybean in the southeastern United States.
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Affiliation(s)
- J L Blount
- UGA Griffin, UGA Entomology, Griffin, GA, USA
- Corresponding author
| | - P M Roberts
- UGA Tifton, UGA Entomology, Horticulture Bldg., Tifton, GA, USA
| | - M D Toews
- UGA Tifton, UGA Entomology, Entomology Annex, Tifton, GA, USA
| | - W A Gardner
- UGA Griffin, UGA Experimental Statistics, Griffin, GA, USA
| | - G D Buntin
- UGA Griffin, UGA Experimental Statistics, Griffin, GA, USA
| | - J W Davis
- UGA Entomology, UGA Athens, 413 Biological Sciences Bldg., Athens, GA, USA
| | - J N All
- UGA Entomology, UGA Athens, 413 Biological Sciences Bldg., Athens, GA, USA
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10
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Padilla J, Thorne PK, Martin JS, Rector RS, Akter S, Davis JW, Laughlin MH, Jenkins NT. Transcriptomic effects of metformin in skeletal muscle arteries of obese insulin-resistant rats. Exp Biol Med (Maywood) 2017; 242:617-624. [PMID: 28114814 DOI: 10.1177/1535370216689825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We examined the effects of metformin, a commonly used antidiabetic drug, on gene expression in multiple arteries. Specifically, transcriptional profiles of feed arteries and second branch order arterioles in the soleus, gastrocnemius, and diaphragm muscles as well as aortic endothelial scrapes were examined from obese insulin-resistant Otsuka Long-Evans Tokushima Fatty rats treated with ( n = 9) or without ( n = 10) metformin from 20 to 32 weeks of age. Metformin-treated rats exhibited a reduction in body weight, adiposity, and HbA1c ( P < 0.05). The greatest number of differentially expressed genes (FDR < 15%) between those treated with and without metformin was found in the red gastrocnemius 2a arterioles (93 genes), followed by the diaphragm 2a arterioles (62 genes), and soleus 2a arterioles (15 genes). We also found that two genes were differentially expressed in aortic endothelial cells (LETMD1 and HMGCS2, both downregulated), one gene in the gastrocnemius feed artery (BLNK, downregulated), and no genes in the soleus and diaphragm feed arteries and white gastrocnemius 2a arterioles. No single gene was altered by metformin across all vessels examined. This study provides evidence that metformin treatment produces distinct gene expression effects throughout the arterial tree in a rat model of obesity and insulin resistance. Genes whose expression was modulated with metformin do not appear to have a clear connection with its known mechanisms of action. These findings support the notion that vascular gene regulation in response to oral pharmacological therapy, such as metformin, is vessel specific. Impact statement This study provides evidence that metformin treatment produces artery-specific gene expression effects. The genes whose expression was modulated with metformin do not appear to have a clear connection with its known mechanisms of action.
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Affiliation(s)
- Jaume Padilla
- 1 Nutrition and Exercise Physiology, University of Missouri, Columbia, MO 65211, USA.,2 Child Health, University of Missouri, Columbia, MO 65211, USA.,3 Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA
| | - Pamela K Thorne
- 4 Biomedical Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Jeffrey S Martin
- 5 Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine, Auburn, AL 36832, USA.,6 School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | - R Scott Rector
- 1 Nutrition and Exercise Physiology, University of Missouri, Columbia, MO 65211, USA.,7 Research Service-Harry S Truman Memorial VA Medical Center, Columbia, MO 65211, USA.,8 Medicine-Division of Gastroenterology and Hepatology, University of Missouri, Columbia, MO 65211, USA
| | - Sadia Akter
- 9 MU Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - J Wade Davis
- 9 MU Informatics Institute, University of Missouri, Columbia, MO 65211, USA.,10 Health Management and Informatics, University of Missouri, Columbia, MO 65211, USA.,11 Statistics, University of Missouri, Columbia, MO 65211, USA
| | - M Harold Laughlin
- 3 Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA.,4 Biomedical Sciences, University of Missouri, Columbia, MO 65211, USA.,12 Medical Pharmacology and Physiology, University of Missouri, Columbia, MO 65211, USA
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11
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Almamun M, Kholod O, Stuckel AJ, Levinson BT, Johnson NT, Arthur GL, Davis JW, Taylor KH. Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemia. Leuk Lymphoma 2017; 58:1-12. [PMID: 28094574 DOI: 10.1080/10428194.2016.1272683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A complete understanding of the mechanisms involved in the development of pre-B ALL is lacking. In this study, we integrated DNA methylation data and gene expression data to elucidate the impact of aberrant intergenic DNA methylation on gene expression in pre-B ALL. We found a subset of differentially methylated intergenic loci that were associated with altered gene expression in pre-B ALL patients. Notably, 84% of these regions were also bound by transcription factors (TF) known to play roles in differentiation and B-cell development in a lymphoblastoid cell line. Further, an overall downregulation of eRNA transcripts was observed in pre-B ALL patients and these transcripts were associated with the downregulation of putative target genes involved in B-cell migration, proliferation, and apoptosis. The identification of novel putative regulatory regions highlights the significance of intergenic DNA sequences and may contribute to the identification of new therapeutic targets for the treatment of pre-B ALL.
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Olha Kholod
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Alexei J Stuckel
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Benjamin T Levinson
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Nathan T Johnson
- b Bioinformatics and Computational Biology , Worcester Polytechnic Institute , Worcester , MA , USA
| | - Gerald L Arthur
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - J Wade Davis
- c Department of Health Management and Informatics , University of Missouri-Columbia , Columbia , MO , USA
| | - Kristen H Taylor
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
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12
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Liu M, Davis JW, Idler KB, Mostafa NM, Okun MM, Waring JF. Genetic analysis of NCSTN for potential association with hidradenitis suppurativa in familial and nonfamilial patients. Br J Dermatol 2016; 175:414-6. [PMID: 26879264 DOI: 10.1111/bjd.14482] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2016] [Indexed: 01/26/2023]
Affiliation(s)
- M Liu
- Pharmacogenetics and Pharmacogenomics, AbbVie Inc., One N. Waukegan Road, North Chicago, IL, 60064, U.S.A
| | - J W Davis
- Pharmacogenetics and Pharmacogenomics, AbbVie Inc., One N. Waukegan Road, North Chicago, IL, 60064, U.S.A
| | - K B Idler
- Pharmacogenetics and Pharmacogenomics, AbbVie Inc., One N. Waukegan Road, North Chicago, IL, 60064, U.S.A
| | - N M Mostafa
- Research and Development, AbbVie Inc., One N. Waukegan Road, North Chicago, IL, 60064, U.S.A
| | - M M Okun
- Department of Immunology, AbbVie Inc., One N. Waukegan Road, North Chicago, IL, 60064, U.S.A
| | - J F Waring
- Pharmacogenetics and Pharmacogenomics, AbbVie Inc., One N. Waukegan Road, North Chicago, IL, 60064, U.S.A
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13
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Almamun M, Levinson BT, van Swaay AC, Johnson NT, McKay SD, Arthur GL, Davis JW, Taylor KH. Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia. Epigenetics 2016; 10:882-90. [PMID: 26308964 PMCID: PMC4622668 DOI: 10.1080/15592294.2015.1078050] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under the age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered in cancer and impact gene expression. To identify epigenetic alterations in ALL, genome-wide methylation profiles were generated using the methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially methylated regions (DMR) were observed in ALL patients with ∼90% present within intronic or intergenic regions. To determine the regulatory potential of the DMR, whole-transcriptome analysis was performed and integrated with methylation data. Aberrant promoter methylation was associated with the altered expression of genes involved in transcriptional regulation, apoptosis, and proliferation. Novel enhancer-like sequences were identified within intronic and intergenic DMR. Aberrant methylation in these regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis. These genes include potential epi-driver genes, such as SYNE1, PTPRS, PAWR, HDAC9, RGCC, MCOLN2, LYN, TRAF3, FLT1, and MELK, which may provide a selective advantage to leukemic cells. In addition, the differential expression of epigenetic modifier genes, pseudogenes, and non-coding RNAs was also observed accentuating the role of erroneous epigenetic gene regulation in ALL.
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences ; University of Missouri-Columbia ; Columbia , MO USA
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14
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Harper JL, Caesar GA, Pennington KA, Davis JW, Schulz LC. Placental changes caused by food restriction during early pregnancy in mice are reversible. Reproduction 2016; 150:165-72. [PMID: 26060317 DOI: 10.1530/rep-15-0010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In a previous study, 50% calorie restriction in mice from d1.5 to 11.5 of pregnancy resulted in reduced placental weights and areas,relative sparing of labyrinth zone area compared to junctional zone area, and dramatic changes in global gene expression profiles.However, little lasting effect was seen on adult offspring of these pregnancies, with a slight reduction in adiposity in males and some changes in liver gene expression in both sexes. The goals of the present study were to determine whether the placental changes induced by caloric restriction in early pregnancy had permanent, irreversible effects on the placenta, and whether the changes in liver gene expression in adult offspring were present before birth. There were no differences in placental weights or areas, or the areas of individual placental zones near term in mice that had previously been food restricted. Global gene expression profiles at d18.5 were indistinguishable in placentas from control and previously food-restricted mothers. In fetuses from restricted dams at d18.5, liver expression of Gck, a key regulator of glycogen synthesis, was reduced, whereas its expression was increased in livers from adult offspring of restricted dams. Ppara expression was also reduced in fetal livers from restricted dams at d18.5, but not in adult offspring livers. We conclude that alterations in the placenta caused by nutrient restriction in early pregnancy are reversible, and that alterations in gene expression in livers of adult offspring are not a result of changes initiated during pregnancy and maintained through adulthood.
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Affiliation(s)
- Jennifer L Harper
- Department of Obstetrics, Gynecology and Women’s Health, NW509 Health Sciences Center, 2. Division of Biological Sciences and 3Department of Statistics, Department of Health Management Informatics, University of Missouri, 1 Hospital Drive, Columbia, Missouri 65212, USA.
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15
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Waring JF, Dumas EO, Abel S, Coakley E, Cohen DE, Davis JW, Podsadecki T, Dutta S. Serum miR-122 may serve as a biomarker for response to direct acting antivirals: effect of paritaprevir/R with dasabuvir or ombitasvir on miR-122 in HCV-infected subjects. J Viral Hepat 2016; 23:96-104. [PMID: 26436610 DOI: 10.1111/jvh.12470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/27/2015] [Indexed: 12/14/2022]
Abstract
Circulating microRNAs (miRNA) have been intensely investigated as biomarkers in disease and therapy. Several studies have identified miR-122 as an important regulator of HCV replication. The effect of new therapies that directly target the HCV replication life cycle on circulating microRNA levels has not been elucidated. We performed expression profiling of circulating miRNA in serum in subjects treated with HCV direct-acting antiviral agents (DAAs). Serum miRNA levels were evaluated from two studies in HCV GT1-infected treatment-naïve subjects and prior nonresponders to pegylated interferon (pegIFN) and ribavirin (RBV) who received paritaprevir/ritonavir + dasabuvir + RBV for 12 weeks, and in treatment-naïve genotype (GT)1-3-infected subjects who received paritaprevir/ritonavir + ombitasvir ± RBV for 12 weeks. Over 100 different miRNA species were detected in serum. Of these, levels of miR-122 showed the most consistent change in response to treatment across all HCV genotypes. In all subjects, miR-122 showed an average four-fold reduction between baseline and week 2, and remained below baseline through post-treatment week 12 in subjects who achieved sustained virological response. In contrast, in subjects who did not achieve SVR, miR-122 levels began to return to baseline levels after the second week of treatment. The change in miR-122 levels was similar across genotypes, and was comparable with or without RBV. This is the first report comparing expression levels of circulating miRNA in HCV GT1-3 subjects treated with IFN-free combinations of DAAs. The results suggest that serum levels of miR-122 are reduced following treatment in subjects who achieve SVR, and correlate with HCV RNA levels across genotypes.
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Affiliation(s)
- J F Waring
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
| | - E O Dumas
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - S Abel
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
| | - E Coakley
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - D E Cohen
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - J Wade Davis
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
| | - T Podsadecki
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - S Dutta
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
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Hennings JM, Zimmer RL, Nabli H, Davis JW, Sutovsky P, Sutovsky M, Sharpe-Timms KL. Improved Murine Blastocyst Quality and Development in a Single Culture Medium Compared to Sequential Culture Media. Reprod Sci 2015; 23:310-7. [PMID: 26668049 DOI: 10.1177/1933719115618281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Validate single versus sequential culture media for murine embryo development. DESIGN Prospective laboratory experiment. SETTING Assisted Reproduction Laboratory. ANIMALS Murine embryos. INTERVENTIONS Thawed murine zygotes cultured for 3 or 5 days (d3 or d5) in single or sequential embryo culture media developed for human in vitro fertilization. MAIN OUTCOME MEASURES On d3, zygotes developing to the 8 cell (8C) stage or greater were quantified using 4',6-diamidino-2-phenylindole (DAPI), and quality was assessed by morphological analysis. On d5, the number of embryos reaching the blastocyst stage was counted. DAPI was used to quantify total nuclei and inner cell mass nuclei. Localization of ubiquitin C-terminal hydrolase L1 (UCHL1) and ubiquitin C-terminal hydrolase L3 (UCHL3) was reference points for evaluating cell quality. RESULTS Comparing outcomes in single versus to sequential media, the odds of embryos developing to the 8C stage on d3 were 2.34 time greater (P = .06). On d5, more embryos reached the blastocyst stage (P = <.0001), hatched, and had significantly more trophoblast cells (P = .005) contributing to the increased total cell number. Also at d5, localization of distinct cytoplasmic UCHL1 and nuclear UCHL3 was found in high-quality hatching blastocysts. Localization of UCHL1 and UCHL3 was diffuse and inappropriately dispersed throughout the cytoplasm in low-quality nonhatching blastocysts. CONCLUSIONS Single medium yields greater cell numbers, an increased growth rate, and more hatching of murine embryos. Cytoplasmic UCHL1 and nuclear UHCL3 localization patterns were indicative of embryo quality. Our conclusions are limited to murine embryos but one might speculate that single medium may also be more beneficial for human embryo culture. Human embryo studies are needed.
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Affiliation(s)
- Justin M Hennings
- Division of Reproductive and Perinatal Research, Department of Obstetrics, Gynecology and Women's Health, School of Medicine, Columbia, MO, USA Division of Animal Sciences, College of Agriculture, Food and Natural Resources, Columbia, MO, USA
| | - Randall L Zimmer
- Division of Reproductive and Perinatal Research, Department of Obstetrics, Gynecology and Women's Health, School of Medicine, Columbia, MO, USA
| | - Henda Nabli
- Division of Reproductive and Perinatal Research, Department of Obstetrics, Gynecology and Women's Health, School of Medicine, Columbia, MO, USA
| | - J Wade Davis
- Department of Health Management and Informatics, School of Medicine, The University of Missouri, Columbia, MO, USA Department of Statistics, College of Arts and Sciences, The University of Missouri, Columbia, MO, USA Biostatistics and Research Design, Galena Hall, Columbia, MO, USA
| | - Peter Sutovsky
- Division of Reproductive and Perinatal Research, Department of Obstetrics, Gynecology and Women's Health, School of Medicine, Columbia, MO, USA Division of Animal Sciences, College of Agriculture, Food and Natural Resources, Columbia, MO, USA
| | - Miriam Sutovsky
- Division of Animal Sciences, College of Agriculture, Food and Natural Resources, Columbia, MO, USA
| | - Kathy L Sharpe-Timms
- Division of Reproductive and Perinatal Research, Department of Obstetrics, Gynecology and Women's Health, School of Medicine, Columbia, MO, USA Division of Animal Sciences, College of Agriculture, Food and Natural Resources, Columbia, MO, USA
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17
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McIntyre JK, Davis JW, Hinman C, Macneale KH, Anulacion BF, Scholz NL, Stark JD. Soil bioretention protects juvenile salmon and their prey from the toxic impacts of urban stormwater runoff. Chemosphere 2015; 132:213-9. [PMID: 25576131 DOI: 10.1016/j.chemosphere.2014.12.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 05/14/2023]
Abstract
Green stormwater infrastructure (GSI), or low impact development, encompasses a diverse and expanding portfolio of strategies to reduce the impacts of stormwater runoff on natural systems. Benchmarks for GSI success are usually framed in terms of hydrology and water chemistry, with reduced flow and loadings of toxic chemical contaminants as primary metrics. Despite the central goal of protecting aquatic species abundance and diversity, the effectiveness of GSI treatments in maintaining diverse assemblages of sensitive aquatic taxa has not been widely evaluated. In the present study we characterized the baseline toxicity of untreated urban runoff from a highway in Seattle, WA, across six storm events. For all storms, first flush runoff was toxic to the daphniid Ceriodaphnia dubia, causing up to 100% mortality or impairing reproduction among survivors. We then evaluated whether soil media used in bioretention, a conventional GSI method, could reduce or eliminate toxicity to juvenile coho salmon (Oncorhynchus kisutch) as well as their macroinvertebrate prey, including cultured C. dubia and wild-collected mayfly nymphs (Baetis spp.). Untreated highway runoff was generally lethal to salmon and invertebrates, and this acute mortality was eliminated when the runoff was filtered through soil media in bioretention columns. Soil treatment also protected against sublethal reproductive toxicity in C. dubia. Thus, a relatively inexpensive GSI technology can be highly effective at reversing the acutely lethal and sublethal effects of urban runoff on multiple aquatic species.
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Affiliation(s)
- J K McIntyre
- Washington State University, Puyallup Research and Extension Center, Puyallup, WA, USA.
| | - J W Davis
- U.S. Fish & Wildlife Service, Washington Fish and Wildlife Office, Lacey, WA, USA
| | - C Hinman
- Washington State University, Puyallup Research and Extension Center, Puyallup, WA, USA
| | - K H Macneale
- National Ocean and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Seattle, WA, USA
| | - B F Anulacion
- National Ocean and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Seattle, WA, USA
| | - N L Scholz
- National Ocean and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Seattle, WA, USA
| | - J D Stark
- Washington State University, Puyallup Research and Extension Center, Puyallup, WA, USA
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18
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Abstract
DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182–200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.
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Key Words
- CG dinucleotide
- CLP, common lymphoid progenitor cells
- CpGI, CpG island
- DMRs, differentially methylated regions
- DNA methylation
- FDR, false discovery rate.
- H3K27ac, histone H3 lysine 27 acetylation
- H3K4me1, histone H3 lysine 4 monomethylation
- HCB, human umbilical cord blood
- HSCs, haematopoietic stem cells
- MBDs, methyl CpG binding domains
- MIRA-seq, methylated CpG island recovery assay (MIRA) followed by next generation sequencing
- MeCP2, methyl CpG binding protein 2
- Pre-B, precursor B-cell; CD
- Pro-B, progenitor B-cell
- ROIs, regions of interest
- TFs, transcription factors
- acute lymphoblastic leukemia; CpG
- cluster of differentiation; ALL
- enhancer
- next-generation sequencing
- precursor B-cell
- umbilical cord blood
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences ; University of Missouri-Columbia ; Columbia , MO USA
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19
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Laughlin MH, Padilla J, Jenkins NT, Thorne PK, Martin JS, Rector RS, Akter S, Davis JW. Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats. J Appl Physiol (1985) 2015; 119:604-16. [PMID: 26183478 DOI: 10.1152/japplphysiol.00317.2015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/10/2015] [Indexed: 12/20/2022] Open
Abstract
We employed next-generation, transcriptome-wide RNA sequencing (RNA-Seq) technology to assess the effects of two different exercise training protocols on transcriptional profiles in diaphragm second-order arterioles (D2a) and in the diaphragm feed artery (DFA) from Otsuka Long Evans Tokushima Fatty (OLETF) rats. Arterioles were isolated from the diaphragm of OLETF rats that underwent an endurance exercise training program (EX; n = 13), interval sprint training program (SPRINT; n = 14), or remained sedentary (Sed; n = 12). Our hypothesis was that exercise training would have similar effects on gene expression in the diaphragm and soleus muscle arterioles because diaphragm blood flow increases during exercise to a similar extent as in soleus. Results reveal that several canonical pathways that were significantly altered by exercise in limb skeletal muscles were not among the pathways significantly changed in the diaphragm arterioles including actin cytoskeleton signaling, role of NFAT in regulation of immune response, protein kinase A signaling, and protein ubiquitination pathway. EX training altered the expression of a smaller number of genes than did SPRINT in the DFA but induced a larger number of genes with altered expression in the D2a than did SPRINT. In fact, FDR differential expression analysis (FDR, 10%) indicated that only two genes exhibited altered expression in D2a of SPRINT rats. Very few of the genes that exhibited altered expression in the DFA or D2a were also altered in limb muscle arterioles. Finally, results indicate that the 2a arterioles of soleus muscle (S2a) from endurance-trained animals and the DFA of SPRINT animals exhibited the largest number of genes with altered expression.
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Affiliation(s)
- M Harold Laughlin
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri; Biomedical Sciences, University of Missouri, Columbia, Missouri; Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri
| | - Jaume Padilla
- Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri; Child Health, University of Missouri, Columbia, Missouri; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | | | - Pamela K Thorne
- Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Jeffrey S Martin
- Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn Campus, Auburn, Alabama; Kinesiology, Auburn University, Auburn, Alabama
| | - R Scott Rector
- Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri; Research Service-Harry S Truman Memorial VA Medical Center, Columbia, Missouri; Internal Medicine-Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri
| | - Sadia Akter
- MU Informatics Institute, University of Missouri, Columbia, Missouri; and
| | - J Wade Davis
- Health Management and Informatics, University of Missouri, Columbia, Missouri; Statistics, University of Missouri, Columbia, Missouri; MU Informatics Institute, University of Missouri, Columbia, Missouri; and
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20
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Laughlin MH, Padilla J, Jenkins NT, Thorne PK, Martin JS, Rector RS, Akter S, Davis JW. Exercise-induced differential changes in gene expression among arterioles of skeletal muscles of obese rats. J Appl Physiol (1985) 2015; 119:583-603. [PMID: 26183477 DOI: 10.1152/japplphysiol.00316.2015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/10/2015] [Indexed: 02/01/2023] Open
Abstract
Using next-generation, transcriptome-wide RNA sequencing (RNA-Seq) technology we assessed the effects of exercise training on transcriptional profiles in skeletal muscle arterioles isolated from the soleus and gastrocnemius muscles of Otsuka Long Evans Tokushima Fatty (OLETF) rats that underwent an endurance exercise training program (EX; n = 13), interval sprint training program (SPRINT; n = 14), or remained sedentary (Sed; n = 12). We hypothesized that the greatest effects of exercise would be in the gastrocnemius arterioles. Results show that EX caused the largest number of changes in gene expression in the soleus and white gastrocnemius 2a arterioles with little to no changes in the feed arteries. In contrast, SPRINT caused substantial changes in gene expression in the feed arteries. IPA canonical pathway analysis revealed 18 pathways with significant changes in gene expression when analyzed across vessels and revealed that EX induces increased expression of the following genes in all arterioles examined: Shc1, desert hedgehog protein (Dhh), adenylate cyclase 4 (Adcy4), G protein binding protein, alpha (Gnat1), and Bcl2l1 and decreased expression of ubiquitin D (Ubd) and cAMP response element modulator (Crem). EX increased expression of endothelin converting enzyme (Ece1), Hsp90b, Fkbp5, and Cdcl4b in four of five arterioles. SPRINT had effects on expression of Crem, Dhh, Bcl2l1, and Ubd that were similar to EX. SPRINT also increased expression of Nfkbia, Hspa5, Tubb 2a and Tubb 2b, and Fkbp5 in all five arterioles and increased expression of Gnat1 in all but the soleus second-order arterioles. Many contractile and/or structural protein genes were increased by SPRINT in the gastrocnemius feed artery, but the same genes exhibited decreased expression in red gastrocnemius arterioles. We conclude that training-induced changes in arteriolar gene expression patterns differ by muscle fiber type composition and along the arteriolar tree.
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Affiliation(s)
- M Harold Laughlin
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri; Biomedical Sciences, University of Missouri, Columbia, Missouri; Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri
| | - Jaume Padilla
- Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri; Child Health, University of Missouri, Columbia, Missouri; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | | | - Pamela K Thorne
- Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Jeffrey S Martin
- Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn Campus, Auburn, Alabama; Kinesiology, Auburn University, Auburn, Alabama
| | - R Scott Rector
- Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri; Research Service-Harry S Truman Memorial Veterans Affairs Medical Center, Columbia, Missouri; Medicine-Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri
| | - Sadia Akter
- Statistics, University of Missouri, Columbia, Missouri
| | - J Wade Davis
- Health Management and Informatics, University of Missouri, Columbia, Missouri; Statistics, University of Missouri, Columbia, Missouri; MU Informatics Institute, University of Missouri, Columbia, Missouri; and
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21
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Techasintana P, Davis JW, Gubin MM, Magee JD, Atasoy U. Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells. PLoS One 2015; 10:e0129321. [PMID: 26162078 PMCID: PMC4498740 DOI: 10.1371/journal.pone.0129321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 05/07/2015] [Indexed: 11/30/2022] Open
Abstract
Due to poor correlation between steady state mRNA levels and protein product, purely transcriptomic profiling methods may miss genes posttranscriptionally regulated by RNA binding proteins (RBPs) and microRNAs (miRNAs). RNA immunoprecipitation (RIP) methods developed to identify in vivo targets of RBPs have greatly elucidated those mRNAs which may be regulated via transcript stability and translation. The RBP HuR (ELAVL1) and family members are major stabilizers of mRNA. Many labs have identified HuR mRNA targets; however, many of these analyses have been performed in cell lines and oftentimes are not independent biological replicates. Little is known about how HuR target mRNAs behave in conditional knock-out models. In the present work, we performed HuR RIP-Seq and RNA-Seq to investigate HuR direct and indirect targets using a novel conditional knock-out model of HuR genetic ablation during CD4+ T activation and Th2 differentiation. Using independent biological replicates, we generated a high coverage RIP-Seq data set (>160 million reads) that was analyzed using bioinformatics methods specifically designed to find direct mRNA targets in RIP-Seq data. Simultaneously, another set of independent biological replicates were sequenced by RNA-Seq (>425 million reads) to identify indirect HuR targets. These direct and indirect targets were combined to determine canonical pathways in CD4+ T cell activation and differentiation for which HuR plays an important role. We show that HuR may regulate genes in multiple canonical pathways involved in T cell activation especially the CD28 family signaling pathway. These data provide insights into potential HuR-regulated genes during T cell activation and immune mechanisms.
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Affiliation(s)
- Patsharaporn Techasintana
- Department of Surgery, University of Missouri, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - J. Wade Davis
- Department of Biostatistics, University of Missouri, Columbia, Missouri, United States of America
| | - Matthew M. Gubin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Joseph D. Magee
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, United States of America
| | - Ulus Atasoy
- Department of Surgery, University of Missouri, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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22
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Zurita AJ, Pisters LL, Wang X, Troncoso P, Dieringer P, Ward JF, Davis JW, Pettaway CA, Logothetis CJ, Pagliaro LC. Integrating chemohormonal therapy and surgery in known or suspected lymph node metastatic prostate cancer. Prostate Cancer Prostatic Dis 2015; 18:276-80. [PMID: 26171883 DOI: 10.1038/pcan.2015.23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/12/2015] [Accepted: 04/08/2015] [Indexed: 11/09/2022]
Abstract
BACKGROUND Prostate cancer persisting in the primary site after systemic therapy may contribute to emergence of resistance and progression. We previously demonstrated molecular characteristics of lethal cancer in the prostatectomy specimens of patients presenting with lymph node metastasis after chemohormonal treatment. Here we report the post-treatment outcomes of these patients and assess whether a link exists between surgery and treatment-free/cancer-free survival. METHODS Patients with either clinically detected lymph node metastasis or primaries at high risk for nodal dissemination were treated with androgen ablation and docetaxel. Those responding with PSA concentration <1 ng ml(-1) were recommended surgery 1 year from enrollment. ADT was withheld postoperatively. The rate of survival without biochemical progression 1 year after surgery was measured to screen for efficacy. RESULTS Forty patients were enrolled and 39 were evaluable. Three patients (7.7%) declined surgery. Of the remaining 36, 4 patients experienced disease progression during treatment and 4 more did not reach PSA <1. Twenty-six patients (67%) completed surgery, and 13 (33%) were also progression-free 1 year postoperatively (8 with undetectable PSA). With a median follow-up of 61 months, time to treatment failure was 27 months in the patients undergoing surgery. The most frequent patterns of first disease recurrence were biochemical (10 patients) and systemic (5). CONCLUSIONS Half of the patients undergoing surgery were off treatment and progression-free 1 year following completion of all therapy. These results suggest that integration of surgery is feasible and may be superior to systemic therapy alone for selected prostate cancer patients presenting with nodal metastasis.
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Affiliation(s)
- A J Zurita
- Department of Genitourinary Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - L L Pisters
- Department of Urology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - X Wang
- Department of Biostatistics, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - P Troncoso
- Department of Pathology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - P Dieringer
- Department of Genitourinary Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - J F Ward
- Department of Urology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - J W Davis
- Department of Urology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - C A Pettaway
- Department of Urology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - C J Logothetis
- Department of Genitourinary Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - L C Pagliaro
- Department of Genitourinary Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
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23
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Ericsson AC, Davis JW, Spollen W, Bivens N, Givan S, Hagan CE, McIntosh M, Franklin CL. Effects of vendor and genetic background on the composition of the fecal microbiota of inbred mice. PLoS One 2015; 10:e0116704. [PMID: 25675094 PMCID: PMC4326421 DOI: 10.1371/journal.pone.0116704] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/12/2014] [Indexed: 02/07/2023] Open
Abstract
The commensal gut microbiota has been implicated as a determinant in several human diseases and conditions. There is mounting evidence that the gut microbiota of laboratory mice (Mus musculus) similarly modulates the phenotype of mouse models used to study human disease and development. While differing model phenotypes have been reported using mice purchased from different vendors, the composition and uniformity of the fecal microbiota in mice of various genetic backgrounds from different vendors is unclear. Using culture-independent methods and robust statistical analysis, we demonstrate significant differences in the richness and diversity of fecal microbial populations in mice purchased from two large commercial vendors. Moreover, the abundance of many operational taxonomic units, often identified to the species level, as well as several higher taxa, differed in vendor- and strain-dependent manners. Such differences were evident in the fecal microbiota of weanling mice and persisted throughout the study, to twenty-four weeks of age. These data provide the first in-depth analysis of the developmental trajectory of the fecal microbiota in mice from different vendors, and a starting point from which researchers may be able to refine animal models affected by differences in the gut microbiota and thus possibly reduce the number of animals required to perform studies with sufficient statistical power.
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Affiliation(s)
- Aaron C. Ericsson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
- Mutant Mouse Resource and Research Center, University of Missouri, Columbia, Missouri, United States of America
- University of Missouri Metagenomics Center, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
| | - J. Wade Davis
- Department of Biostatistics, University of Missouri, Columbia, Missouri, United States of America
| | - William Spollen
- Informatics Research Core Facility, University of Missouri, Columbia, Missouri, United States of America
| | - Nathan Bivens
- DNA Core Facility, University of Missouri, Columbia, Missouri, United States of America
| | - Scott Givan
- Informatics Research Core Facility, University of Missouri, Columbia, Missouri, United States of America
| | - Catherine E. Hagan
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - Mark McIntosh
- DNA Core Facility, University of Missouri, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - Craig L. Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
- Mutant Mouse Resource and Research Center, University of Missouri, Columbia, Missouri, United States of America
- University of Missouri Metagenomics Center, University of Missouri, Columbia, Missouri, United States of America
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24
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Miller DL, Davis JW, Taylor KH, Johnson J, Shi Z, Williams R, Atasoy U, Lewis JS, Stack MS. Identification of a human papillomavirus-associated oncogenic miRNA panel in human oropharyngeal squamous cell carcinoma validated by bioinformatics analysis of the Cancer Genome Atlas. Am J Pathol 2015; 185:679-92. [PMID: 25572154 DOI: 10.1016/j.ajpath.2014.11.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/03/2014] [Accepted: 11/12/2014] [Indexed: 12/19/2022]
Abstract
High-risk human papillomavirus (HPV) is a causative agent for an increasing subset of oropharyngeal squamous cell carcinomas (OPSCCs), and current evidence supports these tumors as having identifiable risk factors and improved response to therapy. However, the biochemical and molecular alterations underlying the pathobiology of HPV-associated OPSCC (designated HPV(+) OPSCC) remain unclear. Herein, we profile miRNA expression patterns in HPV(+) OPSCC to provide a more detailed understanding of pathologic molecular events and to identify biomarkers that may have applicability for early diagnosis, improved staging, and prognostic stratification. Differentially expressed miRNAs were identified in RNA isolated from an initial clinical cohort of HPV(+/-) OPSCC tumors by quantitative PCR-based miRNA profiling. This oncogenic miRNA panel was validated using miRNA sequencing and clinical data from The Cancer Genome Atlas and miRNA in situ hybridization. The HPV-associated oncogenic miRNA panel has potential utility in diagnosis and disease stratification and in mechanistic elucidation of molecular factors that contribute to OPSCC development, progression, and differential response to therapy.
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Affiliation(s)
- Daniel L Miller
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri
| | - J Wade Davis
- Department of Health Management and Informatics, University of Missouri School of Medicine, Columbia, Missouri; Department of Statistics, University of Missouri School of Medicine, Columbia, Missouri
| | - Kristen H Taylor
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri
| | - Jeff Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, Indiana; Harper Cancer Research Institute, University of Notre Dame, South Bend, Indiana
| | - Zonggao Shi
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, Indiana; Harper Cancer Research Institute, University of Notre Dame, South Bend, Indiana
| | - Russell Williams
- Department of Biochemistry, Indiana University South Bend, South Bend, Indiana
| | - Ulus Atasoy
- Department of Surgery, University of Missouri School of Medicine, Columbia, Missouri
| | - James S Lewis
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri; Department of Otolaryngology Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - M Sharon Stack
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, Indiana; Harper Cancer Research Institute, University of Notre Dame, South Bend, Indiana.
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McIntyre JK, Davis JW, Incardona JP, Stark JD, Anulacion BF, Scholz NL. Zebrafish and clean water technology: assessing soil bioretention as a protective treatment for toxic urban runoff. Sci Total Environ 2014; 500-501:173-80. [PMID: 25217993 DOI: 10.1016/j.scitotenv.2014.08.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/14/2014] [Accepted: 08/19/2014] [Indexed: 05/07/2023]
Abstract
Urban stormwater contains a complex mixture of contaminants that can be acutely toxic to aquatic biota. Green stormwater infrastructure (GSI) is a set of evolving technologies intended to reduce impacts on natural systems by slowing and filtering runoff. The extent to which GSI methods work as intended is usually assessed in terms of water quantity (hydrology) and quality (chemistry). Biological indicators of GSI effectiveness have received less attention, despite an overarching goal of protecting the health of aquatic species. Here we use the zebrafish (Danio rerio) experimental model to evaluate bioinfiltration as a relatively inexpensive technology for treating runoff from an urban highway with dense motor vehicle traffic. Zebrafish embryos exposed to untreated runoff (48-96h; six storm events) displayed an array of developmental abnormalities, including delayed hatching, reduced growth, pericardial edema, microphthalmia (small eyes), and reduced swim bladder inflation. Three of the six storms were acutely lethal, and sublethal toxicity was evident across all storms, even when stormwater was diluted by as much as 95% in clean water. As anticipated from exposure to cardiotoxic polycyclic aromatic hydrocarbons (PAHs), untreated runoff also caused heart failure, as indicated by circulatory stasis, pericardial edema, and looping defects. Bioretention treatment dramatically improved stormwater quality and reversed nearly all forms of developmental toxicity. The zebrafish model therefore provides a versatile experimental platform for rapidly assessing GSI effectiveness.
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Affiliation(s)
- J K McIntyre
- Washington State University Puyallup Research & Extension Center, 2606W Pioneer Ave, Puyallup, WA 98371, USA.
| | - J W Davis
- U.S. Fish & Wildlife Service Washington Fish & Wildlife Office, 510 Desmond Dr. SE, Lacey, WA 98503, USA
| | - J P Incardona
- NOAA-NMFS Northwest Science Center, 2725 Montlake Blvd E, Seattle, WA 98112, USA
| | - J D Stark
- Washington State University Puyallup Research & Extension Center, 2606W Pioneer Ave, Puyallup, WA 98371, USA
| | - B F Anulacion
- NOAA-NMFS Northwest Science Center, 2725 Montlake Blvd E, Seattle, WA 98112, USA
| | - N L Scholz
- NOAA-NMFS Northwest Science Center, 2725 Montlake Blvd E, Seattle, WA 98112, USA
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Uhlich RM, Konie JA, Davis JW, Misfeldt ML, Nelson C, Calaluce R, Barnes SL. Novel microRNA correlations in the severely injured. Surgery 2014; 156:834-40. [PMID: 25239329 DOI: 10.1016/j.surg.2014.06.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/19/2014] [Indexed: 12/16/2022]
Abstract
PURPOSE Severe injury initiates an inflammatory response that can perpetuate immunological dysfunction, uncontrolled inflammation, and subsequent multisystem organ failure. MicroRNAs (miRNAs) have recently been identified as regulators of this inflammatory response. Our study sought to identify the differential expression of unique miRNAs and their correlations with genes of the Toll-like receptor (TLR) pathways, and clinical parameters in the severely injured. METHODS Fourteen trauma patients requiring transfusion were prospectively enrolled in this institutional review board-approved study. Inclusion criteria consisted of adult patients deemed clinically to be in hemorrhagic shock necessitating transfusion in the acute phase of their injury care. Peripheral blood samples were obtained after admission to the surgical intensive care unit. Expression of circulating mature miRNA from each patient, as well as from 10 healthy, age-matched controls, was determined and compared using the HiSeq 2500 sequencing system and the R software system. Gene expression of TLR signaling pathways for each patient was examined using custom gene expression polymerase chain reaction arrays. Statistical analyses were performed using general linear models and empirical Bayes methods to determine differential expression and Spearman's nonparametric correlation analysis. RESULTS Subjects were 21-77 years old (mean, 42), 80% male, Injury Severity Score 11-43 (mean, 26), with 11 blunt and 3 penetrating injuries. Three were intubated and 5 received blood products before arrival. Base deficit upon hospital admission was 3 to 20 (mean, 9). All patients required blood transfusion secondary to blood loss sustained during injury. Survival to discharge was 93%. Controls were 27-64 years old (mean, 40) and 60% male. Sequencing analysis revealed 69 differentially expressed miRNAs (P < .05) in the severely injured. Within the differentially expressed miRNAs, there were 12 direct and 6 indirect correlations with multiple genes involved in the TLR3 and TLR4 signaling pathways. The relationships between these same miRNAs and clinical parameters were also analyzed. We discovered 4 direct correlations with base deficit and HCO3, and 7 indirect correlations involving total fresh frozen plasma transfused, base deficit, HCO3, and PaCO2 levels. CONCLUSION Differential expression and correlations between miRNAs, genes of the TLR pathways, and clinical parameters are unique findings in the severely injured and may lead to a greater understanding of the regulation of sterile inflammation after severe injury.
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Affiliation(s)
- Rindi M Uhlich
- Department of Surgery, University of Missouri, Columbia, MO
| | - Jared A Konie
- Department of Surgery, University of Missouri, Columbia, MO
| | - J Wade Davis
- Department of Health Management and Informatics, University of Missouri, Columbia, MO
| | - Michael L Misfeldt
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO
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Padilla J, Jenkins NT, Thorne PK, Martin JS, Rector RS, Davis JW, Laughlin MH. Identification of genes whose expression is altered by obesity throughout the arterial tree. Physiol Genomics 2014; 46:821-32. [PMID: 25271210 DOI: 10.1152/physiolgenomics.00091.2014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We used next-generation RNA sequencing (RNA-Seq) technology on the whole transcriptome to identify genes whose expression is consistently affected by obesity across multiple arteries. Specifically, we examined transcriptional profiles of the iliac artery as well as the feed artery, first, second, and third branch order arterioles in the soleus, gastrocnemius, and diaphragm muscles from obese Otsuka Long-Evans Tokushima Fatty (OLETF) and lean Long-Evans Tokushima Otsuka (LETO) rats. Within the gastrocnemius and soleus muscles, the number of genes differentially expressed with obesity tended to increase with increasing branch order arteriole number (i.e., decreasing size of the artery). This trend was opposite in the diaphragm. We found a total of 15 genes that were consistently upregulated with obesity (MIS18A, CTRB1, FAM151B, FOLR2, PXMP4, OAS1B, SREBF2, KLRA17, SLC25A44, SNX10, SLFN3, MEF2BNB, IRF7, RAD23A, LGALS3BP) and five genes that were consistently downregulated with obesity (C2, GOLGA7, RIN3, PCP4, CYP2E1). A small fraction (∼9%) of the genes affected by obesity was modulated across all arteries examined. In conclusion, the present study identifies a select number of genes (i.e., 20 genes) whose expression is consistently altered throughout the arterial network in response to obesity and provides further insight into the heterogeneous vascular effects of obesity. Although there is no known direct function of the majority of 20 genes related to vascular health, the obesity-associated upregulation of SREBF2, LGALS3BP, IRF7, and FOLR2 across all arteries is suggestive of an unfavorable vascular phenotypic alteration with obesity. These data may serve as an important resource for identifying novel therapeutic targets against obesity-related vascular complications.
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Affiliation(s)
- Jaume Padilla
- Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri; Child Health, University of Missouri, Columbia, Missouri; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri;
| | | | - Pamela K Thorne
- Biomedical Sciences, University of Missouri, Columbia, Missouri
| | | | - R Scott Rector
- Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri; Research Service-Harry S Truman Memorial VA Medical Center, Columbia, Missouri; Medicine-Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri
| | - J Wade Davis
- Health Management and Informatics, University of Missouri, Columbia, Missouri; Statistics, University of Missouri, Columbia, Missouri; MU Informatics Institute, University of Missouri, Columbia, Missouri; and
| | - M Harold Laughlin
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri; Biomedical Sciences, University of Missouri, Columbia, Missouri; Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri
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Cook LC, Hillhouse AE, Myles MH, Lubahn DB, Bryda EC, Davis JW, Franklin CL. The role of estrogen signaling in a mouse model of inflammatory bowel disease: a Helicobacter hepaticus model. PLoS One 2014; 9:e94209. [PMID: 24709804 PMCID: PMC3978010 DOI: 10.1371/journal.pone.0094209] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 03/13/2014] [Indexed: 12/23/2022] Open
Abstract
The pathogenesis of inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, is due in part to interactions between the immune system, genetics, the environment, and endogenous microbiota. Gonadal sex hormones (GSH), such as estrogen, are thought to be involved in the development of IBD as variations in disease severity occur during pregnancy, menopause, or oral contraceptives use. In certain strains of mice, infection with Helicobacter hepaticus triggers IBD-like mucosal inflammation that is more severe in female mice than in males, suggesting a role for GSH in this model. To determine the role of estrogen signaling in microbiota-induced intestinal inflammation, estrogen receptor (ER) α and β knock-out (KO) mice, ER agonists, and adoptive transfers were utilized. We demonstrate that, when signaling is limited to ERβ on a non-CD4+ cell subset, disease is less severe and this correlates with decreased expression of pro-inflammatory mediators.
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Affiliation(s)
- Lydia C. Cook
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - Andrew E. Hillhouse
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - Matthew H. Myles
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
- IDEXX Laboratories, Columbia, Missouri, United States of America
| | - Dennis B. Lubahn
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Elizabeth C. Bryda
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - J. Wade Davis
- Departments of Health Management and Informatics, and Statistics, University of Missouri, Columbia, Missouri, United States of America
| | - Craig L. Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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Kassotis CD, Tillitt DE, Davis JW, Hormann AM, Nagel SC. Estrogen and androgen receptor activities of hydraulic fracturing chemicals and surface and ground water in a drilling-dense region. Endocrinology 2014; 155:897-907. [PMID: 24424034 DOI: 10.1210/en.2013-1697] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The rapid rise in natural gas extraction using hydraulic fracturing increases the potential for contamination of surface and ground water from chemicals used throughout the process. Hundreds of products containing more than 750 chemicals and components are potentially used throughout the extraction process, including more than 100 known or suspected endocrine-disrupting chemicals. We hypothesized that a selected subset of chemicals used in natural gas drilling operations and also surface and ground water samples collected in a drilling-dense region of Garfield County, Colorado, would exhibit estrogen and androgen receptor activities. Water samples were collected, solid-phase extracted, and measured for estrogen and androgen receptor activities using reporter gene assays in human cell lines. Of the 39 unique water samples, 89%, 41%, 12%, and 46% exhibited estrogenic, antiestrogenic, androgenic, and antiandrogenic activities, respectively. Testing of a subset of natural gas drilling chemicals revealed novel antiestrogenic, novel antiandrogenic, and limited estrogenic activities. The Colorado River, the drainage basin for this region, exhibited moderate levels of estrogenic, antiestrogenic, and antiandrogenic activities, suggesting that higher localized activity at sites with known natural gas-related spills surrounding the river might be contributing to the multiple receptor activities observed in this water source. The majority of water samples collected from sites in a drilling-dense region of Colorado exhibited more estrogenic, antiestrogenic, or antiandrogenic activities than reference sites with limited nearby drilling operations. Our data suggest that natural gas drilling operations may result in elevated endocrine-disrupting chemical activity in surface and ground water.
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Affiliation(s)
- Christopher D Kassotis
- Department of Obstetrics, Gynecology and Women's Health and Division of Biological Sciences (C.D.K., A.M.H., S.C.N.), University of Missouri, Columbia, Missouri 65211; US Geological Survey (D.E.T.), Columbia Environmental Research Center, Columbia, Missouri 65201; and Departments of Statistics and Health Management and Informatics (J.W.D.), University of Missouri, Columbia, Missouri 65211
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Jenkins NT, Padilla J, Thorne PK, Martin JS, Rector RS, Davis JW, Laughlin MH. Transcriptome-wide RNA sequencing analysis of rat skeletal muscle feed arteries. I. Impact of obesity. J Appl Physiol (1985) 2014; 116:1017-32. [PMID: 24436298 DOI: 10.1152/japplphysiol.01233.2013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We employed next-generation RNA sequencing (RNA-Seq) technology to determine the influence of obesity on global gene expression in skeletal muscle feed arteries. Transcriptional profiles of the gastrocnemius and soleus muscle feed arteries (GFA and SFA, respectively) and aortic endothelial cell-enriched samples from obese Otsuka Long-Evans Tokushima Fatty (OLETF) and lean Long-Evans Tokushima Otsuka (LETO) rats were examined. Obesity produced 282 upregulated and 133 downregulated genes in SFA and 163 upregulated and 77 downregulated genes in GFA [false discovery rate (FDR) < 10%] with an overlap of 93 genes between the arteries. In LETO rats, there were 89 upregulated and 114 downregulated genes in the GFA compared with the SFA. There were 244 upregulated and 275 downregulated genes in OLETF rats (FDR < 10%) in the GFA compared with the SFA, with an overlap of 76 differentially expressed genes common to both LETO and OLETF rats in both the GFA and SFA. A total of 396 transcripts were found to be differentially expressed between LETO and OLETF in aortic endothelial cell-enriched samples. Overall, we found 1) the existence of heterogeneity in the transcriptional profile of the SFA and GFA within healthy LETO rats, 2) that this between-vessel heterogeneity was markedly exacerbated in the hyperphagic, obese OLETF rat, and 3) a greater number of genes whose expression was altered by obesity in the SFA compared with the GFA. Also, results indicate that in OLETF rats the GFA takes on a relatively more proatherogenic phenotype compared with the SFA.
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Affiliation(s)
- Nathan T Jenkins
- Department of Kinesiology, University of Georgia, Athens, Georgia
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Padilla J, Jenkins NT, Thorne PK, Martin JS, Rector RS, Davis JW, Laughlin MH. Transcriptome-wide RNA sequencing analysis of rat skeletal muscle feed arteries. II. Impact of exercise training in obesity. J Appl Physiol (1985) 2014; 116:1033-47. [PMID: 24408995 DOI: 10.1152/japplphysiol.01234.2013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We employed next-generation RNA sequencing (RNA-Seq) technology to determine the extent to which exercise training alters global gene expression in skeletal muscle feed arteries and aortic endothelial cells of obese Otsuka Long-Evans Tokushima Fatty (OLETF) rats. Transcriptional profiles of the soleus and gastrocnemius muscle feed arteries (SFA and GFA, respectively) and aortic endothelial cell-enriched samples from rats that underwent an endurance exercise training program (EndEx; n = 12) or a interval sprint training program (IST; n = 12) or remained sedentary (Sed; n = 12) were examined. In response to EndEx, there were 39 upregulated (e.g., MANF) and 20 downregulated (e.g., ALOX15) genes in SFA and 1 upregulated (i.e., Wisp2) and 1 downregulated (i.e., Crem) gene in GFA [false discovery rate (FDR) < 10%]. In response to IST, there were 305 upregulated (e.g., MANF, HSPA12B) and 324 downregulated genes in SFA and 101 upregulated and 66 downregulated genes in GFA, with an overlap of 32 genes between arteries. Furthermore, in aortic endothelial cells, there were 183 upregulated (e.g., eNOS, SOD-3) and 141 downregulated (e.g., ATF3, Clec1b, npy, leptin) genes with EndEx and 71 upregulated and 69 downregulated genes with IST, with an overlap of 35 between exercise programs. Expression of only two genes (Tubb2b and Slc9a3r2) was altered (i.e., increased) by exercise in all three arteries. The finding that both EndEx and IST produced greater transcriptional changes in the SFA compared with the GFA is intriguing when considering the fact that treadmill bouts of exercise are associated with greater relative increases in blood flow to the gastrocnemius muscle compared with the soleus muscle.
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Affiliation(s)
- Jaume Padilla
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri
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Marshall KD, Edwards MA, Krenz M, Davis JW, Baines CP. Proteomic mapping of proteins released during necrosis and apoptosis from cultured neonatal cardiac myocytes. Am J Physiol Cell Physiol 2014; 306:C639-47. [PMID: 24401845 DOI: 10.1152/ajpcell.00167.2013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cardiac injury induces myocyte apoptosis and necrosis, resulting in the secretion and/or release of intracellular proteins. Currently, myocardial injury can be detected by analysis of a limited number of biomarkers in blood or coronary artery perfusate. However, the complete proteomic signature of protein release from necrotic cardiac myocytes is unknown. Therefore, we undertook a proteomic-based study of proteins released from cultured neonatal rat cardiac myocytes in response to H2O2 (necrosis) or staurosporine (apoptosis) to identify novel specific markers of cardiac myocyte cell death. Necrosis and apoptosis resulted in the identification of 147 and 79 proteins, respectively. Necrosis resulted in a relative increase in the amount of many proteins including the classical necrotic markers lactate dehydrogenase (LDH), high-mobility group B1 (HMGB1), myoglobin, enolase, and 14-3-3 proteins. Additionally, we identified several novel markers of necrosis including HSP90, α-actinin, and Trim72, many of which were elevated over control levels earlier than classical markers of necrotic injury. In contrast, the majority of identified proteins remained at low levels during apoptotic cell death, resulting in no candidate markers for apoptosis being identified. Blotting for a selection of these proteins confirmed their release during necrosis but not apoptosis. We were able to confirm the presence of classical necrotic markers in the extracellular milieu of necrotic myocytes. We also were able to identify novel markers of necrotic cell death with relatively early release profiles compared with classical protein markers of necrosis. These results have implications for the discovery of novel biomarkers of necrotic myocyte injury, especially in the context of ischemia-reperfusion injury.
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Affiliation(s)
- Kurt D Marshall
- Department of Biomedical Sciences, University of Missouri-Columbia, Columbia, Missouri
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Wakefield BJ, Koopman RJ, Keplinger LE, Bomar M, Bernt B, Johanning JL, Kruse RL, Davis JW, Wakefield DS, Mehr DR. Effect of home telemonitoring on glycemic and blood pressure control in primary care clinic patients with diabetes. Telemed J E Health 2014; 20:199-205. [PMID: 24404819 DOI: 10.1089/tmj.2013.0151] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE Patient self-management support may be augmented by using home-based technologies that generate data points that providers can potentially use to make more timely changes in the patients' care. The purpose of this study was to evaluate the effectiveness of short-term targeted use of remote data transmission on treatment outcomes in patients with diabetes who had either out-of-range hemoglobin A1c (A1c) and/or blood pressure (BP) measurements. MATERIALS AND METHODS A single-center randomized controlled clinical trial design compared in-home monitoring (n=55) and usual care (n=53) in patients with type 2 diabetes and hypertension being treated in primary care clinics. Primary outcomes were A1c and systolic BP after a 12-week intervention. RESULTS There were no significant differences between the intervention and control groups on either A1c or systolic BP following the intervention. CONCLUSIONS The addition of technology alone is unlikely to lead to improvements in outcomes. Practices need to be selective in their use of telemonitoring with patients, limiting it to patients who have motivation or a significant change in care, such as starting insulin. Attention to the need for effective and responsive clinic processes to optimize the use of the additional data is also important when implementing these types of technology.
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Padilla J, Jenkins NT, Lee S, Zhang H, Cui J, Zuidema MY, Zhang C, Hill MA, Perfield JW, Ibdah JA, Booth FW, Davis JW, Laughlin MH, Rector RS. Vascular transcriptional alterations produced by juvenile obesity in Ossabaw swine. Physiol Genomics 2013; 45:434-46. [PMID: 23592636 DOI: 10.1152/physiolgenomics.00038.2013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We adopted a transcriptome-wide microarray analysis approach to determine the extent to which vascular gene expression is altered as a result of juvenile obesity and identify obesity-responsive mRNAs. We examined transcriptional profiles in the left anterior descending coronary artery (LAD), perivascular fat adjacent to the LAD, and descending thoracic aorta between obese (n = 5) and lean (n = 6) juvenile Ossabaw pigs (age = 22 wk). Obesity was experimentally induced by feeding the animals a high-fat/high-fructose corn syrup/high-cholesterol diet for 16 wk. We found that expression of 189 vascular cell genes in the LAD and expression of 165 genes in the thoracic aorta were altered with juvenile obesity (false discovery rate ≤ 10%) with an overlap of only 28 genes between both arteries. Notably, a number of genes found to be markedly upregulated in the LAD of obese pigs are implicated in atherosclerosis, including ACP5, LYZ, CXCL14, APOE, PLA2G7, LGALS3, SPP1, ITGB2, CYBB, and P2RY12. Furthermore, pathway analysis revealed the induction of proinflammatory and pro-oxidant pathways with obesity primarily in the LAD. Gene expression in the LAD perivascular fat was minimally altered with juvenile obesity. Together, we provide new evidence that obesity produces artery-specific changes in pretranslational regulation with a clear upregulation of proatherogenic genes in the LAD. Our data may offer potential viable drug targets and mechanistic insights regarding the molecular precursors involved in the origins of overnutrition and obesity-associated vascular disease. In particular, our results suggest that the oxidized LDL/LOX-1/NF-κB signaling axis may be involved in the early initiation of a juvenile obesity-induced proatherogenic coronary artery phenotype.
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Affiliation(s)
- Jaume Padilla
- Biomedical Sciences, University of Missouri, Columbia, Missouri 65211, USA.
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Bender SB, Davis JW, Rector RS, Laughlin MH, Sowers JR. Characterization of the coronary vascular transcriptome in a rat model of metabolic syndrome. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.lb645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shawn B Bender
- Internal Medicine/EndocrinologyUniversity of MissouriColumbiaMO
- Harry S Truman Memorial Veterans HospitalColumbiaMO
| | - J. Wade Davis
- Health Management and InformaticsUniversity of MissouriColumbiaMO
| | - R. Scott Rector
- Internal Medicine/EndocrinologyUniversity of MissouriColumbiaMO
- Harry S Truman Memorial Veterans HospitalColumbiaMO
| | | | - James R Sowers
- Internal Medicine/EndocrinologyUniversity of MissouriColumbiaMO
- Harry S Truman Memorial Veterans HospitalColumbiaMO
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Rahmatpanah FB, Carstens S, Hooshmand SI, Welsh EC, Sjahputera O, Taylor KH, Bennett LB, Shi H, Davis JW, Arthur GL, Shanafelt TD, Kay NE, Wooldridge JE, Caldwell CW. Large-scale analysis of DNA methylation in chronic lymphocytic leukemia. Epigenomics 2012; 1:39-61. [PMID: 20495622 DOI: 10.2217/epi.09.10] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
AIMS B-cell chronic lymphocytic leukemia (CLL) is a heterogeneous malignancy that clinically ranges from indolent to rapidly progressive. CLL, like other cancers, can be affected by epigenetic alterations. MATERIALS & METHODS A microarray discovery-based study was initiated to determine DNA methylation in CLL cases with a range of CD38 expression (1–92%). RESULTS Many loci were either methylated or unmethylated across all CD38 levels, but differential methylation was also observed for some genes. Genomic sequencing of DLEU7 confirmed extensive cytosine methylation preferentially in patient samples with low CD38 expression, whereas NRP2, SFRP2 and ADAM12 were more commonly methylated in those with high CD38 expression. CONCLUSION This study demonstrates that CLL is affected by CpG island methylation in some genes that segregate with CD38 expression levels, while most others show similar methylation patterns across all levels. The CpG island methylation in certain functional gene groups and pathway-associated genes that are known to be deregulated in CLL provides additional insights into the CLL methylome and epigenetic contribution to cellular dysfunction. It will now be useful to investigate the effectiveness of epigenetic therapeutic reversal of these alterations to develop effective treatments for the disease.
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Affiliation(s)
- Farahnaz B Rahmatpanah
- Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, Missouri 65212, USA
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Roberts MD, Childs TE, Brown JD, Davis JW, Booth FW. Early depression of Ankrd2 and Csrp3 mRNAs in the polyribosomal and whole tissue fractions in skeletal muscle with decreased voluntary running. J Appl Physiol (1985) 2012; 112:1291-9. [PMID: 22282489 DOI: 10.1152/japplphysiol.01419.2011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The wheel-lock (WL) model for depressed ambulatory activity in rats has shown metabolic maladies ensuing within 53-173 h after WL begins. We sought to determine if WL beginning after 21-23 days of voluntary running in growing female Wistar rats affected the mRNA profile in the polyribosomal fraction from plantaris muscle shortly following WL. In experiment 1, WL occurred at 0200 and muscles were harvested at 0700 daily at 5 h (WL5h, n = 4), 29 h (WL29h, n = 4), or 53 h (WL53h, n = 4) after WL. Affymetrix Rat Gene 1.0 ST Arrays were used to test the initial question as to whether WL affects mRNA occupancy on skeletal muscle polyribosomes. Using a false discovery rate of 15%, no changes in mRNAs in the polyribosomal fraction were observed at WL29h and eight mRNAs (of over 8,200 identified targets) were altered at WL53h compared with WL5h. Interestingly, two of the six downregulated genes included ankyrin repeat domain 2 (Ankrd2) and cysteine-rich protein 3/muscle LIM protein (Csrp3), both of which encode mechanical stretch sensors and RT-PCR verified their WL-induced decline. In experiment 2, whole muscle mRNA and protein levels were analyzed for Ankrd2 and Csrp3 from the muscles of WL5h (4 original samples + 2 new), WL29h (4 original), WL53h (4 original + 2 new), as well as WL173 h (n = 6 new) and animals that never ran (SED, 4-5 new). Relative to WL5h controls, whole tissue Ankrd2 and Csrp3 mRNAs were lower (P < 0.05) at WL53h, WL173h, and SED; Ankrd2 protein tended to decrease at WL53h (P = 0.054) and Csrp3 protein was less in WL173h and SED rats (P < 0.05). In summary, unique early declines in Ankrd2 and Csrp3 mRNAs were identified with removal of voluntary running, which was subsequently followed by declines in Csrp3 protein levels during longer periods of wheel lock.
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Affiliation(s)
- Michael D Roberts
- Department of Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
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Wakefield BJ, Hayes J, Boren SA, Pak Y, Davis JW. Strain and satisfaction in caregivers of veterans with chronic illness. Res Nurs Health 2011; 35:55-69. [DOI: 10.1002/nur.21456] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2011] [Indexed: 11/08/2022]
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Padilla J, Simmons GH, Davis JW, Whyte JJ, Zderic TW, Hamilton MT, Bowles DK, Laughlin MH. Impact of exercise training on endothelial transcriptional profiles in healthy swine: a genome-wide microarray analysis. Am J Physiol Heart Circ Physiol 2011; 301:H555-64. [PMID: 21622830 DOI: 10.1152/ajpheart.00065.2011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
While the salutary effects of exercise training on conduit artery endothelial cells have been reported in animals and humans with cardiovascular risk factors or disease, whether a healthy endothelium is alterable with exercise training is less certain. The purpose of this study was to evaluate the impact of exercise training on transcriptional profiles in normal endothelial cells using a genome-wide microarray analysis. Brachial and internal mammary endothelial gene expression was compared between a group of healthy pigs that exercise trained for 16-20 wk (n = 8) and a group that remained sedentary (n = 8). We found that a total of 130 genes were upregulated and 84 genes downregulated in brachial artery endothelial cells with exercise training (>1.5-fold and false discovery rate <15%). In contrast, a total of 113 genes were upregulated and 31 genes downregulated in internal mammary artery endothelial cells using the same criteria. Although there was an overlap of 66 genes (59 upregulated and 7 downregulated with exercise training) between the brachial and internal mammary arteries, the identified endothelial gene networks and biological processes influenced by exercise training were distinctly different between the brachial and internal mammary arteries. These data indicate that a healthy endothelium is indeed responsive to exercise training and support the concept that the influence of physical activity on endothelial gene expression is not homogenously distributed throughout the vasculature.
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Affiliation(s)
- Jaume Padilla
- Dept. of Biomedical Sciences, E102 Veterinary Medicine, 1600 E. Rollins Rd., Univ. of Missouri, Columbia, MO 65211, USA.
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Padilla J, Simmons GH, Davis JW, Zderic TW, Hamilton MT, Laughlin MH. Impact of Exercise Training on Endothelial Transcriptional Profiles in Healthy Swine: A Genome-wide Microarray Analysis. Med Sci Sports Exerc 2011. [DOI: 10.1249/01.mss.0000402057.51942.2c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Punke JP, Fox DB, Tomlinson JL, Davis JW, Mann FA. Acetabular Ventroversion with Double Pelvic Osteotomy Versus Triple Pelvic Osteotomy: A Cadaveric Study in Dogs. Vet Surg 2011; 40:555-62. [DOI: 10.1111/j.1532-950x.2011.00802.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Coberly E, Boren SA, Davis JW, McConnell AL, Chitima-Matsiga R, Ge B, Logan RA, Steinmann WC, Hodge RH. Linking clinic patients to Internet-based, condition-specific information prescriptions. J Med Libr Assoc 2010; 98:160-4. [PMID: 20428282 DOI: 10.3163/1536-5050.98.2.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Emily Coberly
- School of Medicine, University of Missouri, Columbia, MO 65212, USA.
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Gubin MM, Calaluce R, Davis JW, Magee JD, Strouse CS, Shaw DP, Ma L, Brown A, Hoffman T, Rold TL, Atasoy U. Overexpression of the RNA binding protein HuR impairs tumor growth in triple negative breast cancer associated with deficient angiogenesis. Cell Cycle 2010; 9:3337-46. [PMID: 20724828 DOI: 10.4161/cc.9.16.12711] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Interactions between RNA binding proteins (RBPs) and genes are not well understood, especially in regulation of angiogenesis. The RBP HuR binds to the AU-rich (ARE) regions of labile mRNAs, facilitating their translation into protein and has been hypothesized to be a tumor-maintenance gene. Elevated levels of cytoplasmic HuR directly correlate with increased invasiveness and poor prognosis for many cancers, including those of the breast. HuR controls the expression of multiple genes involved in angiogenesis including VEGFα, HIF1α and thrombospondin 1 (TSP1). We investigated the role of HuR in estrogen receptor negative (ER(-)) breast cancer. MDA-MB-231 cells with higher levels of HuR have alterations in cell cycle kinetics and faster growth. Unexpectedly, HuR overexpression significantly interfered with tumor growth in orthotopic mouse models. The putative mechanism seems to be an anti-angiogenetic effect by increasing expression of TSP1 but also surprisingly, downregulating VEGF, a target which HuR normally increases. Our findings reveal that HuR may be regulating a cluster of genes involved in blood vessel formation which controls tumor angiogenesis. An approach of modulating HuR levels may overcome limitations associated with monotherapies targeting tumor vessel formation.
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Affiliation(s)
- Matthew M Gubin
- Department of Surgery, University of Missouri, Columbia, Missouri, USA
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Sharpe-Timms KL, Nabli H, Zimmer RL, Birt JA, Davis JW. Inflammatory cytokines differentially up-regulate human endometrial haptoglobin production in women with endometriosis. Hum Reprod 2010; 25:1241-50. [PMID: 20176595 PMCID: PMC2902841 DOI: 10.1093/humrep/deq032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 01/08/2010] [Accepted: 01/25/2010] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Evidence suggests that eutopic endometrium from women with endometriosis (US-E) has intrinsic functional anomalies compared with women without endometriosis (US-C). We hypothesized that differences in endometrial haptoglobin (eHp) mRNA and protein levels exist between eutopic endometrium from US-E and US-C and that inflammatory mediators may be involved. METHODS Endometrial stromal cells and tissue explants from US-E (n = 18) and US-C (n = 18) were cultured (24 h/48 h for cells/explants) with interleukin (IL)-1alpha, -1beta, -6, -8 or tumor necrosis factor-alpha (TNF-alpha) at 0-100 ng/ml. eHp protein in media and mRNA levels were quantified by enzyme-linked immunosorbent assay and quantitative PCR. RESULTS In eutopic endometrial stromal cells from US-E, IL-1beta, IL-6 and TNF-alpha (10 ng/ml) increased eHp mRNA levels (P = 0.002, P < 0.001 and P < 0.001, respectively) and eHp protein (P = 0.023, 0.031 and 0.006, respectively) versus control. In endometrial tissues from US-E, IL-1beta, IL-6 and TNF-alpha increased eHp mRNA (P < 0.001, P = 0.017 and P < 0.001, respectively) and eHp protein (P < 0.001, P = 0.007 and 0.039, respectively) versus control. IL-1alpha and IL-8 had small or no effects on isolated endometrial cells or tissues. In US-C, IL-1beta, IL-8 and TNF-alpha each reduced eHp mRNA in endometrial stromal cells (all P < 0.001) versus control; IL-1alpha and IL-6 had no effect. eHp mRNA increased in endometrial tissues from US-C in response to IL-1beta (P = 0.008), IL-6 (P = 0.015) and TNF-alpha (P = 0.031) versus control; IL-1alpha or IL-8 had no effect. CONCLUSIONS Endometrium from US-E differentially responds to specific inflammatory cytokines by production of eHp. We propose that up-regulation of endometrial eHp by inflammatory mediators disrupts normal endometrial function and may facilitate the pathogenesis of endometriosis.
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Affiliation(s)
- K L Sharpe-Timms
- Department of Obstetrics, Gynecology and Women's Health, The University of Missouri-Columbia, 1 Hospital Drive, N 625 HSC, Columbia, MO 65212, USA.
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Calaluce R, Gubin MM, Davis JW, Magee JD, Chen J, Kuwano Y, Gorospe M, Atasoy U. The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer. BMC Cancer 2010; 10:126. [PMID: 20370918 PMCID: PMC2856550 DOI: 10.1186/1471-2407-10-126] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 04/06/2010] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The discordance between steady-state levels of mRNAs and protein has been attributed to posttranscriptional control mechanisms affecting mRNA stability and translation. Traditional methods of genome wide microarray analysis, profiling steady-state levels of mRNA, may miss important mRNA targets owing to significant posttranscriptional gene regulation by RNA binding proteins (RBPs). METHODS The ribonomic approach, utilizing RNA immunoprecipitation hybridized to microarray (RIP-Chip), provides global identification of putative endogenous mRNA targets of different RBPs. HuR is an RBP that binds to the AU-rich elements (ARE) of labile mRNAs, such as proto-oncogenes, facilitating their translation into protein. HuR has been shown to play a role in cancer progression and elevated levels of cytoplasmic HuR directly correlate with increased invasiveness and poor prognosis for many cancers, including those of the breast. HuR has been described to control genes in several of the acquired capabilities of cancer and has been hypothesized to be a tumor-maintenance gene, allowing for cancers to proliferate once they are established. RESULTS We used HuR RIP-Chip as a comprehensive and systematic method to survey breast cancer target genes in both MCF-7 (estrogen receptor positive, ER+) and MDA-MB-231 (estrogen receptor negative, ER-) breast cancer cell lines. We identified unique subsets of HuR-associated mRNAs found individually or in both cell types. Two novel HuR targets, CD9 and CALM2 mRNAs, were identified and validated by quantitative RT-PCR and biotin pull-down analysis. CONCLUSION This is the first report of a side-by-side genome-wide comparison of HuR-associated targets in wild type ER+ and ER- breast cancer. We found distinct, differentially expressed subsets of cancer related genes in ER+ and ER- breast cancer cell lines, and noted that the differential regulation of two cancer-related genes by HuR was contingent upon the cellular environment.
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Affiliation(s)
- Robert Calaluce
- Department of Surgery, University of Missouri, Columbia, Missouri 65212, USA
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Ghosh S, Koblinski J, Johnson J, Liu Y, Ericsson A, Davis JW, Shi Z, Ravosa MJ, Crawford S, Frazier S, Stack MS. Urinary-type plasminogen activator receptor/alpha 3 beta 1 integrin signaling, altered gene expression, and oral tumor progression. Mol Cancer Res 2010; 8:145-58. [PMID: 20145038 DOI: 10.1158/1541-7786.mcr-09-0045] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Oral squamous cell carcinoma (OSCC) has 50% 5-year survival rate, highlighting our limited understanding of the molecular events that contribute to disease progression. Microarray analyses of primary oral tumors have identified urinary-type plasminogen activator (uPA) and its receptor (uPAR) as key genes associated with human OSCC progression. The uPAR functions as both a proteinase receptor and an integrin ligand, modifying proteolysis, migration, integrin signaling, and cellular transcription. In the current study, uPAR expression levels were modified in OSCC cells followed by analysis of tumor growth in an in vivo orthotopic xenograft model and by transcriptional profiling. Overexpression of uPAR resulted in more infiltrative and less differentiated tumors, with ill-defined borders, cytologic atypia, and enhanced vascularity. Analysis of serial sections of both murine experimental tumors and microarrayed human OSCC showed a statistically significant association between uPAR and alpha(3) integrin colocalization in areas exhibiting extracellular signal-regulated kinase phosphorylation, suggesting that uPAR/alpha(3) integrin interaction potentiates extracellular signal-regulated kinase signaling in vivo. This is supported by cDNA microarray analysis, which showed differential expression of 148 genes (113 upregulated and 35 downregulated). Validation of gene expression changes in human OSCC using immunohistochemistry and quantitative real-time PCR showed increased growth factors, proteinases/inhibitors, and matrix components in uPAR-overexpressing tumors. Together, these results support a model wherein increased uPAR expression promotes alpha(3)beta(1) integrin association, resulting in increased mitogen-activated protein kinase signaling and transcriptional activation, leading to the formation of more aggressive tongue tumors. This combined approach has efficacy to identify additional biomarkers and/or prognostic indicators associated with aggressive human OSCC.
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Affiliation(s)
- Supurna Ghosh
- Department of Surgery, Northwestern University Feinberg Medical School, Chicago, Illinois, USA
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Wakefield DS, Brokel J, Ward MM, Schwichtenberg T, Groath D, Kolb M, Davis JW, Crandall D. An exploratory study measuring verbal order content and context. Qual Saf Health Care 2009; 18:169-73. [DOI: 10.1136/qshc.2008.029827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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CHOUDHURY MAHUA, Pandey RS, Clemens DL, Davis JW, Lim RW, Shukla SD. Silencing of histone acetyltransferase GCN5 affects gene expression in human hepatoma cells: A gene array analysis. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.585.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- MAHUA CHOUDHURY
- MEDICAL PHARMACOLOGY AND PHYSIOLOGYUNIVERSITY OF MISSOURICOLUMBIAMO
| | - Ravi S Pandey
- MEDICAL PHARMACOLOGY AND PHYSIOLOGYUNIVERSITY OF MISSOURICOLUMBIAMO
| | - Dahn L Clemens
- Department of Internal MedicineUniversity of Nebraska Medical Centre Veterans Affairs Medical CenterOMAHANE
| | - J Wade Davis
- Department of StatisticsUNIVERSITY OF MISSOURICOLUMBIAMO
| | - Robert W Lim
- MEDICAL PHARMACOLOGY AND PHYSIOLOGYUNIVERSITY OF MISSOURICOLUMBIAMO
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McLean AG, Davis JW, Stangeby PC, Brooks NH, Ellis RM, Haasz AA, Rudakov DL, West WP, Whyte DG, Wong CPC. Porous plug gas injection systems for studies of hydrocarbon dissociation and transport in the DIII-D tokamak. Rev Sci Instrum 2009; 80:043501. [PMID: 19405654 DOI: 10.1063/1.3100180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A probe has been designed, constructed, and successfully used to inject methane into the DIII-D lower divertor in a manner imitating natural release by chemical erosion. This porous plug injector (PPI) probe consists of a self-contained gas reservoir with an integrated pressure gauge and a 3 cm diameter porous surface through which gas is injected into the lower divertor of the tokamak. The probe is positioned flush with the divertor target surface by means of the divertor materials evaluation system. Two gas delivery systems were developed: in the first, gas flow is regulated by a remotely controlled microvalve and in the second by a fixed micro-orifice flow restrictor. Because of the large area of the porous surface through which gas is admitted, the injected hydrocarbon molecules see a local carbon surface (>90% carbon) similar to that seen by hydrocarbons being emitted by chemical sputtering from surrounding carbon tiles. The distributed gas source also reduces the disturbance to the local plasma while providing sufficient signal for spectroscopic detection. In situ spectroscopic measurements with the PPI in DIII-D allow the direct calibration of response for measured plasma conditions from a known influx of gas.
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Affiliation(s)
- A G McLean
- Institute for Aerospace Studies, University of Toronto, 4925 Dufferin St., Toronto, Ontario M3H 5T6, Canada.
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