Project description:The aim of this study was to identify genes, gene clusters and networks involved in sexual dimorphism and in the response to nutritional restriction in porcine skeletal muscles, through the analysis of gene expression differences. Full sib Iberian piglets from three litters composed of two males and two females per family were randomly assigned to two dietary treatments which differed in the feeding level during 15 wk. At the end of the trial, 27 wk of age, significant phenotypic differences were detected between genders and between feeding levels for growth, fatness, fatty acid composition and primary cuts weights. RNA samples from two skeletal muscles, diaphragm and Psoas major, were hybridized with Affymetrix microarrays and the expression data were analyzed using a mixed model and a FDR<0.01. The successfully performed validations by qRT-PCR of six selected genes supported the reliability of our microarray results. Ina a first step, the main gene expression differences between both muscles were established, identifying 181 differentially expressed genes, which represented almost exclusively anatomical structural differences. The analysis between genders reported expression differences of 59 unique genes, mainly implicated in muscle growth and stress response, including well known genes, such as IGF1, apart from others potentially associated to meat quality such as ANKRD1. The analysis of the feeding level effect restriction reported up-regulation of 76 genes and down-regulation of other 60 genes. Functional annotation showed that the moderated nutritional restriction applied led to a reduced growth through down-regulation of key genes implicated in enhancing growth and up-regulation of genes implicated in inhibiting growth. Besides, the restriction led to an increase of muscular aminoacid metabolism and decrease of lipid metabolism as adaptive response. Changes in expression patterns of genes determining meat characteristics, such as PDK4 implicated in water holding, CTSD associated to muscle transformation during meat processing and SCD involved in the determination of fatty acids profiles, were also reported. Finally, we identify relevant expression differences in ADAM12, CA2, UCHL1 and ESRRG genes, which are involved in human obesity and have not been previously studied in pig.

Project description:Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot, we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death. Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot, we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death. 16 liver and subcutaneous backfat samples from eight animals at slaughter, 211 days old, four males and four females, four under high feeding level and four under 20% restriction

Project description:Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot, we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death. Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot, we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death.

Project description:Liver plays major roles in vital functions including responses to energy deprivation. It is known that body composition and fuel metabolism differs between genders. However there are many unclear aspects related to metabolic pathways affected by feeding level and gender, which could be addressed by transcriptome analyses. To date, no published study in porcine liver has investigated the effects of both gender and feeding level on global gene expression level.We performed a gene expression analysis, using microarrays, in hepatic samples of pigs of the obese Iberian breed to analyze feeding level and gender effects. Results showed that feeding level leads to small expression differences, while gender leads to larger ones. Biological interpretation of the differentially expressed genes conditional on feeding level showed an overrepresentation of genes implicated in general metabolic processes, responses to stimulus and stress, oxidoreductase activity, calcium ion binding and lipid, organic acid and carbohydrate metabolisms. We validated the expression difference of PHYHD1 by qRT-PCR; however we could not validate the expression differences of other relevant genes. Curiously, validation of PGK1, considered reference gene, confirmed expression differences conditional on feeding level and gender. The annotation of the differentially expressed probes for gender effect allowed to observe sex-chromosome enrichment and dosage compensation phenomena in liver. Biological interpretation showed overrepresentation of genes related with oxidoreductase and transferase activities, lipid, organic acid, carbohydrate and steroid metabolisms and genes related with metabolites generation and energy and electron transport. Aside from 13 consistently across tissue differentially expressed genes between gender, gender hepatic expression dimorphism of key genes involved in lipid, carbohydrate and protein metabolisms and antioxidant capacity were also detected. A deeper qRT-PCR analysis showed a downregulation in entire males of all major genes implicated in hepatic degradation processes of androstenone and skatole. We have identified changes in hepatic gene expression conditional on feeding and gender. Reduction of around 25% in feeding level do not lead to great differences but gender effect leads not only to a larger number of differentially expressed probes, but much larger expression differences. Validation of microarray results is needed mainly for small expression differences. Experiment Overall Design: Eight liver samples from eight animals at slaughter, 211 days old, four males and four females, four under high feeding level and four under 25% restriction.

Project description:Liver plays major roles in vital functions including responses to energy deprivation. It is known that body composition and fuel metabolism differs between genders. However there are many unclear aspects related to metabolic pathways affected by feeding level and gender, which could be addressed by transcriptome analyses. To date, no published study in porcine liver has investigated the effects of both gender and feeding level on global gene expression level.We performed a gene expression analysis, using microarrays, in hepatic samples of pigs of the obese Iberian breed to analyze feeding level and gender effects. Results showed that feeding level leads to small expression differences, while gender leads to larger ones. Biological interpretation of the differentially expressed genes conditional on feeding level showed an overrepresentation of genes implicated in general metabolic processes, responses to stimulus and stress, oxidoreductase activity, calcium ion binding and lipid, organic acid and carbohydrate metabolisms. We validated the expression difference of PHYHD1 by qRT-PCR; however we could not validate the expression differences of other relevant genes. Curiously, validation of PGK1, considered reference gene, confirmed expression differences conditional on feeding level and gender. The annotation of the differentially expressed probes for gender effect allowed to observe sex-chromosome enrichment and dosage compensation phenomena in liver. Biological interpretation showed overrepresentation of genes related with oxidoreductase and transferase activities, lipid, organic acid, carbohydrate and steroid metabolisms and genes related with metabolites generation and energy and electron transport. Aside from 13 consistently across tissue differentially expressed genes between gender, gender hepatic expression dimorphism of key genes involved in lipid, carbohydrate and protein metabolisms and antioxidant capacity were also detected. A deeper qRT-PCR analysis showed a downregulation in entire males of all major genes implicated in hepatic degradation processes of androstenone and skatole. We have identified changes in hepatic gene expression conditional on feeding and gender. Reduction of around 25% in feeding level do not lead to great differences but gender effect leads not only to a larger number of differentially expressed probes, but much larger expression differences. Validation of microarray results is needed mainly for small expression differences.

Dataset Information

Expression data from porcine diaphragm and Psoas major tissue of Iberian males and females fed with two feeding levels

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