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Cesar ASM, Regitano LCA, Poleti MD, Andrade SCS, Tizioto PC, Oliveira PSN, Felício AM, do Nascimento ML, Chaves AS, Lanna DPD, Tullio RR, Nassu RT, Koltes JE, Fritz-Waters E, Mourão GB, Zerlotini-Neto A, Reecy JM, Coutinho LL. Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content. BMC Genomics 2016; 17:961. [PMID: 27875996 PMCID: PMC5120530 DOI: 10.1186/s12864-016-3306-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 11/17/2016] [Indexed: 12/19/2022] Open
Abstract
Background Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved in several biological functions from transcriptional regulation to physiological processes. Several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. To gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes (DEGs) and functional pathways related to gene expression regulation associated with FA content in cattle. Results Skeletal muscle transcriptome analysis of 164 Nellore steers revealed no differentially expressed genes (DEGs, FDR 10%) for samples with extreme values for linoleic acid (LA) or stearic acid (SA), and only a few DEGs for eicosapentaenoic acid (EPA, 5 DEGs), docosahexaenoic acid (DHA, 4 DEGs) and palmitic acid (PA, 123 DEGs), while large numbers of DEGs were associated with oleic acid (OA, 1134 DEGs) and conjugated linoleic acid cis9 trans11 (CLA-c9t11, 872 DEGs). Functional annotation and functional enrichment from OA DEGs identified important genes, canonical pathways and upstream regulators such as SCD, PLIN5, UCP3, CPT1, CPT1B, oxidative phosphorylation mitochondrial dysfunction, PPARGC1A, and FOXO1. Two important genes associated with lipid metabolism, gene expression and cancer were identified as DEGs between animals with high and low CLA-c9t11, specifically, epidermal growth factor receptor (EGFR) and RNPS. Conclusion Only two out of seven classes of molecules of FA studied were associated with large changes in the expression profile of skeletal muscle. OA and CLA-c9t11 content had significant effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, and cell growth, survival, and migration. These results contribute to our understanding of how some FAs modulate metabolism and may have protective health function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3306-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.,Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | | | - Mirele D Poleti
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Sónia C S Andrade
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.,Departament of Genetics and Evolutionary Biology-IB, USP, São Paulo, SP, 05508-090, Brazil
| | | | | | - Andrezza M Felício
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Amália S Chaves
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Dante P D Lanna
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Rymer R Tullio
- Embrapa Pecuária Sudeste, São Carlos, SP, 13560-970, Brazil
| | - Renata T Nassu
- Embrapa Pecuária Sudeste, São Carlos, SP, 13560-970, Brazil
| | - James E Koltes
- Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Eric Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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Bian Y, Yang Q, Balint-Kurti PJ, Wisser RJ, Holland JB. Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population. BMC Genomics 2014; 15:1068. [PMID: 25475173 PMCID: PMC4300987 DOI: 10.1186/1471-2164-15-1068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022] Open
Abstract
Background A previous study reported a comprehensive quantitative trait locus (QTL) and genome wide association study (GWAS) of southern leaf blight (SLB) resistance in the maize Nested Association Mapping (NAM) panel. Since that time, the genomic resources available for such analyses have improved substantially. An updated NAM genetic linkage map has a nearly six-fold greater marker density than the previous map and the combined SNPs and read-depth variants (RDVs) from maize HapMaps 1 and 2 provided 28.5 M genomic variants for association analysis, 17 fold more than HapMap 1. In addition, phenotypic values of the NAM RILs were re-estimated to account for environment-specific flowering time covariates and a small proportion of lines were dropped due to genotypic data quality problems. Comparisons of original and updated QTL and GWAS results confound the effects of linkage map density, GWAS marker density, population sample size, and phenotype estimates. Therefore, we evaluated the effects of changing each of these parameters individually and in combination to determine their relative impact on marker-trait associations in original and updated analyses. Results Of the four parameters varied, map density caused the largest changes in QTL and GWAS results. The updated QTL model had better cross-validation prediction accuracy than the previous model. Whereas joint linkage QTL positions were relatively stable to input changes, the residual values derived from those QTL models (used as inputs to GWAS) were more sensitive, resulting in substantial differences between GWAS results. The updated NAM GWAS identified several candidate genes consistent with previous QTL fine-mapping results. Conclusions The highly polygenic nature of resistance to SLB complicates the identification of causal genes. Joint linkage QTL are relatively stable to perturbations of data inputs, but their resolution is generally on the order of tens or more Mbp. GWAS associations have higher resolution, but lower power due to stringent thresholds designed to minimize false positive associations, resulting in variability of detection across studies. The updated higher density linkage map improves QTL estimation and, along with a much denser SNP HapMap, greatly increases the likelihood of detecting SNPs in linkage with causal variants. We recommend use of the updated genetic resources and results but emphasize the limited repeatability of small-effect associations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1068) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - James B Holland
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA.
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Bentley AR, Kritchevsky SB, Harris TB, Newman AB, Bauer DC, Meibohm B, Clark AG, Cassano PA. Genetic variation in antioxidant enzymes and lung function. Free Radic Biol Med 2012; 52:1577-83. [PMID: 22387199 PMCID: PMC3390784 DOI: 10.1016/j.freeradbiomed.2012.02.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 02/16/2012] [Accepted: 02/17/2012] [Indexed: 10/28/2022]
Abstract
Not all cigarette smokers develop chronic obstructive pulmonary disease, and discovering susceptibility factors is an important research priority. The oxidative burden of smoking may overwhelm antioxidant defenses, and vulnerabilities may exist as a result of sequence variants in genes encoding antioxidant enzymes. This study explored the association between genetic variation in a network of antioxidant enzymes and lung phenotypes. Linear models evaluated single-locus marker associations in 2387 European American and African American participants in the Health, Aging, and Body Composition Study. After corrections were made for multiple comparisons, 15 statistically significant associations were identified, all of which were for SNP by smoking interactions. The most statistically significant findings were for genes encoding members of the isocitrate dehydrogenase gene family (IDH3A, IDH3B, IDH2). For rs6107100 (IDH3B) the variant genotype was associated with a difference of 6% in the FEV(1)/FVC ratio in African American current smokers, but the SNP had little or no association with FEV(1)/FVC in former and never smokers (nominal p(interaction)=5×10(-6)). A variant of the peroxiredoxin gene (rs9787810, PRDX5) was associated with lower percentage predicted FEV(1) and a lower ratio in European American current smokers, with little or no association in other smoking groups (nominal p(interaction)=0.0001 and 0.0003, respectively). The studied genes have not been reported in previous candidate gene association studies, and thus the findings suggest novel mechanisms and targets for future research and provide evidence for a contribution of sequence variation in genes encoding antioxidant enzymes to susceptibility in smokers.
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Affiliation(s)
- Amy R. Bentley
- Center for Research in Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | | | - Tamara B. Harris
- Intramural Research Program, National Institute on Aging, Bethesda, MD
| | - Anne B. Newman
- Center for Aging and Population Health, University of Pittsburgh, PA
| | - Douglas C. Bauer
- Departments of Medicine and Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
| | | | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY
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Taylor C, Commander CW, Collaco JM, Strug LJ, Li W, Wright FA, Webel AD, Pace RG, Stonebraker JR, Naughton K, Dorfman R, Sandford A, Blackman SM, Berthiaume Y, Paré P, Drumm ML, Zielenski J, Durie P, Cutting GR, Knowles MR, Corey M. A novel lung disease phenotype adjusted for mortality attrition for cystic fibrosis genetic modifier studies. Pediatr Pulmonol 2011; 46:857-69. [PMID: 21462361 PMCID: PMC3130075 DOI: 10.1002/ppul.21456] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 01/20/2011] [Indexed: 11/08/2022]
Abstract
Genetic studies of lung disease in cystic fibrosis (CF) are hampered by the lack of a severity measure that accounts for chronic disease progression and mortality attrition. Further, combining analyses across studies requires common phenotypes that are robust to study design and patient ascertainment. Using data from the North American Cystic Fibrosis Modifier Consortium (Canadian Consortium for CF Genetic Studies, Johns Hopkins University CF Twin and Sibling Study, and University of North Carolina/Case Western Reserve University Gene Modifier Study), the authors calculated age-specific CF percentile values of FEV1 which were adjusted for CF age-specific mortality data. The phenotype was computed for 2,061 patients representing the Canadian CF population, 1,137 extreme phenotype patients in the UNC/Case Western study, and 1,323 patients from multiple CF sib families in the CF Twin and Sibling Study. Despite differences in ascertainment and median age, our phenotype score was distributed in all three samples in a manner consistent with ascertainment differences, reflecting the lung disease severity of each individual in the underlying population. The new phenotype score was highly correlated with the previously recommended complex phenotype, but the new phenotype is more robust for shorter follow-up and for extreme ages. A disease progression and mortality-adjusted phenotype reduces the need for stratification or additional covariates, increasing statistical power, and avoiding possible distortions. This approach will facilitate large-scale genetic and environmental epidemiological studies which will provide targeted therapeutic pathways for the clinical benefit of patients with CF.
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Affiliation(s)
- Chelsea Taylor
- Child Health Evaluative Sciences Program, Hospital for Sick Children, Toronto, Ontario, Canada
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Rancé F, Deschildre A, Bidat E, Just J, Couderc L, Wanin S, Weiss L. [Secondary and tertiary prevention of allergic asthma in children]. Rev Mal Respir 2010; 27:1221-30. [PMID: 21163398 DOI: 10.1016/j.rmr.2010.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 06/29/2010] [Indexed: 11/18/2022]
Abstract
Asthma is a disease of the lung epithelial barrier, most often associated with allergy in children. Asthma and allergy are two distinct diseases, but the phenotypic expression of asthma depends on atopic status. A better definition of phenotypes of asthma would result in better targeting of prevention and treatment modalities. Secondary prevention aims to prevent the onset of asthma and the acquisition of new sensitizations in sensitized children. Studies concerning allergen avoidance are insufficient to reach a definitive conclusion and antihistamines have not been shown to be effective. The results for specific immunotherapy suggest a benefit to prevent transition from allergic rhinitis to asthma and the onset of new sensitizations. Tertiary prevention aims to reduce symptoms in children with an existing allergic asthma diagnosis. The avoidance of known respiratory allergens will only be effective in combination with management of the whole environment. Specific immunotherapy has a real place, in combination with background therapy. It should be used according to guidelines in appropriately treated patients.
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Affiliation(s)
- F Rancé
- TSA 70034, Pôle Médicochirurgical de Pédiatrie, Hôpital des Enfants, 330 Avenue de Grande-Bretagne, 31059 Toulouse Cedex, France.
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