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Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome

BACKGROUND: By comparing fibroblasts collected from animals at 5-months or 16-months of age we have previously found that the cultures from older animals produce much more IL-8 in response to lipopolysaccharide (LPS) stimulation. We now expand this finding by examining whole transcriptome difference...

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Autores principales: Green, Benjamin B, McKay, Stephanie D, Kerr, David E
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312471/
https://www.ncbi.nlm.nih.gov/pubmed/25623529
http://dx.doi.org/10.1186/s12864-015-1223-z
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author Green, Benjamin B
McKay, Stephanie D
Kerr, David E
author_facet Green, Benjamin B
McKay, Stephanie D
Kerr, David E
author_sort Green, Benjamin B
collection PubMed
description BACKGROUND: By comparing fibroblasts collected from animals at 5-months or 16-months of age we have previously found that the cultures from older animals produce much more IL-8 in response to lipopolysaccharide (LPS) stimulation. We now expand this finding by examining whole transcriptome differences in the LPS response between cultures from the same animals at different ages, and also investigate the contribution of DNA methylation to the epigenetic basis for the age-dependent increases in responsiveness. RESULTS: Age-dependent differences in IL-8 production by fibroblasts in response to LPS exposure for 24 h were abolished by pretreatment of cultures with a DNA demethylation agent, 5-aza-2′deoxycytidine (AZA). RNA-Seq analysis of fibroblasts collected from the same individuals at either 5 or 16 months of age and exposed in parallel to LPS for 0, 2, and 8 h revealed a robust response to LPS that was much greater in the cultures from older animals. Pro-inflammatory genes including IL-8, IL-6, TNF-α, and CCL20 (among many other immune associated genes), were more highly expressed (FDR < 0.05) in the 16-month old cultures following LPS exposure. Methylated CpG island recovery assay sequencing (MIRA-Seq) revealed numerous methylation peaks spread across the genome, combined with an overall hypomethylation of gene promoter regions, and a remarkable similarity, except for 20 regions along the genome, between the fibroblasts collected at the two ages from the same animals. CONCLUSIONS: The fibroblast pro-inflammatory response to LPS increases dramatically from 5 to 16 months of age within individual animals. A better understanding of the mechanisms underlying this process could illuminate the physiological processes by which the innate immune response develops and possibly individual variation in innate immune response arises. In addition, although relatively unchanged by age, our data presents a general overview of the bovine fibroblast methylome as a guide for future studies in cattle epigenetics utilizing this cell type. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1223-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-43124712015-02-01 Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome Green, Benjamin B McKay, Stephanie D Kerr, David E BMC Genomics Research Article BACKGROUND: By comparing fibroblasts collected from animals at 5-months or 16-months of age we have previously found that the cultures from older animals produce much more IL-8 in response to lipopolysaccharide (LPS) stimulation. We now expand this finding by examining whole transcriptome differences in the LPS response between cultures from the same animals at different ages, and also investigate the contribution of DNA methylation to the epigenetic basis for the age-dependent increases in responsiveness. RESULTS: Age-dependent differences in IL-8 production by fibroblasts in response to LPS exposure for 24 h were abolished by pretreatment of cultures with a DNA demethylation agent, 5-aza-2′deoxycytidine (AZA). RNA-Seq analysis of fibroblasts collected from the same individuals at either 5 or 16 months of age and exposed in parallel to LPS for 0, 2, and 8 h revealed a robust response to LPS that was much greater in the cultures from older animals. Pro-inflammatory genes including IL-8, IL-6, TNF-α, and CCL20 (among many other immune associated genes), were more highly expressed (FDR < 0.05) in the 16-month old cultures following LPS exposure. Methylated CpG island recovery assay sequencing (MIRA-Seq) revealed numerous methylation peaks spread across the genome, combined with an overall hypomethylation of gene promoter regions, and a remarkable similarity, except for 20 regions along the genome, between the fibroblasts collected at the two ages from the same animals. CONCLUSIONS: The fibroblast pro-inflammatory response to LPS increases dramatically from 5 to 16 months of age within individual animals. A better understanding of the mechanisms underlying this process could illuminate the physiological processes by which the innate immune response develops and possibly individual variation in innate immune response arises. In addition, although relatively unchanged by age, our data presents a general overview of the bovine fibroblast methylome as a guide for future studies in cattle epigenetics utilizing this cell type. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1223-z) contains supplementary material, which is available to authorized users. BioMed Central 2015-01-27 /pmc/articles/PMC4312471/ /pubmed/25623529 http://dx.doi.org/10.1186/s12864-015-1223-z Text en © Green et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Green, Benjamin B
McKay, Stephanie D
Kerr, David E
Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
title Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
title_full Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
title_fullStr Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
title_full_unstemmed Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
title_short Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
title_sort age dependent changes in the lps induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312471/
https://www.ncbi.nlm.nih.gov/pubmed/25623529
http://dx.doi.org/10.1186/s12864-015-1223-z
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