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Identifying molecular effects of diet through systems biology: influence of herring diet on sterol metabolism and protein turnover in mice.

Nookaew I, Gabrielsson BG, Holmäng A, Sandberg AS, Nielsen J - PLoS ONE (2010)

Bottom Line: Changes in lifestyle have resulted in an epidemic development of obesity-related diseases that challenge the healthcare systems worldwide.Our analysis revealed a reduction in sterol metabolism and protein turnover at the transcriptional level in herring-fed mice.This study shows that an integrated analysis of transcriptome data using metabolic networks resulted in the identification of signature pathways.

View Article: PubMed Central - PubMed

Affiliation: Life Sciences/Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.

ABSTRACT

Background: Changes in lifestyle have resulted in an epidemic development of obesity-related diseases that challenge the healthcare systems worldwide. To develop strategies to tackle this problem the focus is on diet to prevent the development of obesity-associated diseases such as cardiovascular disease (CVD). This will require methods for linking nutrient intake with specific metabolic processes in different tissues.

Methodology/principal finding: Low-density lipoprotein receptor-deficient (Ldlr -/-) mice were fed a high fat/high sugar diet to mimic a westernized diet, being a major reason for development of obesity and atherosclerosis. The diets were supplemented with either beef or herring, and matched in macronutrient contents. Body composition, plasma lipids and aortic lesion areas were measured. Transcriptomes of metabolically important tissues, e.g. liver, muscle and adipose tissue were analyzed by an integrated approach with metabolic networks to directly map the metabolic effects of diet in these different tissues. Our analysis revealed a reduction in sterol metabolism and protein turnover at the transcriptional level in herring-fed mice.

Conclusion: This study shows that an integrated analysis of transcriptome data using metabolic networks resulted in the identification of signature pathways. This could not have been achieved using standard clustering methods. In particular, this systems biology analysis could enrich the information content of biomedical or nutritional data where subtle changes in several tissues together affects body metabolism or disease progression. This could be applied to improve diets for subjects exposed to health risks associated with obesity.

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Related in: MedlinePlus

Mapping of metabolic activities in the liver (green and red indicate down- and upregulated based on herring diet, respectively).A. Overview of genes involved in sterol and lipid biosynthesis that are downregulated in response to herring diet. Besides identification of a key reporter GO terms it is also seen that most genes in the biosynthetic pathway towards sterols and fatty acids are downregulated. B. The downregulation (panel A) is further supported by the identification of several reporter metabolites of the cholesterol and fatty acid biosynthesis. C. Measurements of cholesterol and triacylglyceride in the plasma. It is seen that the levels of both are down in the mice fed with the herring diet, and this effect is seen both after 8 and 16 weeks of feeding. D. For all downregulated genes identified in the reporter GO terms (panel A) there was searched for enrichment of transcription factors and microRNAs. The heat map shows identified transcription factors and microRNAs and their co-occurrence matrix. It is observed that most regulatory effects are due to a single factor. For some of the identified transcription factors the corresponding consensus binding sites were identified, and this resulted in identification of consensus binding sites for Srebf (Srebp), Hnf4, Pparg and Ppara. The Ppar systems are important lipid-activated nuclear receptors involved in lipid and glucose metabolism; Pparg is an important transcription factor in adipocytes and Ppara in hepatocytes. Hnf4a is an important regulator of coordinated nuclear receptor-mediated response to xenobiotics through interaction with Cars/Pxr and through Hnf1 it activates the expression of a large number of liver-specific genes, including those involved in glucose, cholesterol, and fatty acid metabolism. The most frequent binding site for microRNAs is the site mmu.miR.103 which implies its contribution to transcriptional inhibition of hepatic lipid synthesis (see Text S1and Figure S7).
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pone-0012361-g003: Mapping of metabolic activities in the liver (green and red indicate down- and upregulated based on herring diet, respectively).A. Overview of genes involved in sterol and lipid biosynthesis that are downregulated in response to herring diet. Besides identification of a key reporter GO terms it is also seen that most genes in the biosynthetic pathway towards sterols and fatty acids are downregulated. B. The downregulation (panel A) is further supported by the identification of several reporter metabolites of the cholesterol and fatty acid biosynthesis. C. Measurements of cholesterol and triacylglyceride in the plasma. It is seen that the levels of both are down in the mice fed with the herring diet, and this effect is seen both after 8 and 16 weeks of feeding. D. For all downregulated genes identified in the reporter GO terms (panel A) there was searched for enrichment of transcription factors and microRNAs. The heat map shows identified transcription factors and microRNAs and their co-occurrence matrix. It is observed that most regulatory effects are due to a single factor. For some of the identified transcription factors the corresponding consensus binding sites were identified, and this resulted in identification of consensus binding sites for Srebf (Srebp), Hnf4, Pparg and Ppara. The Ppar systems are important lipid-activated nuclear receptors involved in lipid and glucose metabolism; Pparg is an important transcription factor in adipocytes and Ppara in hepatocytes. Hnf4a is an important regulator of coordinated nuclear receptor-mediated response to xenobiotics through interaction with Cars/Pxr and through Hnf1 it activates the expression of a large number of liver-specific genes, including those involved in glucose, cholesterol, and fatty acid metabolism. The most frequent binding site for microRNAs is the site mmu.miR.103 which implies its contribution to transcriptional inhibition of hepatic lipid synthesis (see Text S1and Figure S7).

Mentions: In order to identify key biological processes affected by diet in liver, skeletal muscle and WAT, we performed integrated analysis using three biological networks to capture different levels of information. The first analysis provides a global view of the response to diet, identifying significant Gene Ontology (GO)-terms (Figure 2C). We applied the reporter algorithm [4], [14], rather than using the traditional hypogeometric test, since it has the advantage in using the Q-value for all transcripts. The reporter algorithm made it possible to identify key biological processes affected by diet in the three tissues (Figure 2C; for GO “cellular component” and “molecular function” see Figure S4). In liver, the GO biological processes that were affected by diet were related to lipid/sterol metabolism, e.g. “lipid biosynthetic process” (99 transcripts), “sterol biosynthetic process” (25 transcripts) and “cholesterol biosynthetic process” (23 transcripts). Similarly, in muscle and WAT, the GO biological processes affected by diet were translation (321 transcripts, muscle), cell adhesion (419 transcripts, WAT) and defense response to bacterium (77 transcripts, WAT). To further characterize dietary effects on metabolism by the reporter algorithm [4], [14], we also determined key metabolites, using a generic genome-scale metabolic model (GSMM) for mouse [15], and key Reactome processes, using curated evidences from the Reactome database [16]. From this analysis, metabolites related to fatty acid/sterol biosynthesis were identified as the major responses in liver (Figure 3B). Furthermore, specific biological processes related to protein turnover were identified in muscle (Figure 4C). To further identify molecular mechanisms that were triggered by diet, we screened for overrepresentation of regulatory targets, either in the promoter regions or microRNA targets, to identify putative regulatory drivers for the previously identified changes. Hereby, we were able to identify known transcription factors (TFs) and microRNAs that could explain the transcriptional differences in liver and muscle arising from the influence of diet as shown in Figure 3D and Figure S7 (see Text S2 for complete results).


Identifying molecular effects of diet through systems biology: influence of herring diet on sterol metabolism and protein turnover in mice.

Nookaew I, Gabrielsson BG, Holmäng A, Sandberg AS, Nielsen J - PLoS ONE (2010)

Mapping of metabolic activities in the liver (green and red indicate down- and upregulated based on herring diet, respectively).A. Overview of genes involved in sterol and lipid biosynthesis that are downregulated in response to herring diet. Besides identification of a key reporter GO terms it is also seen that most genes in the biosynthetic pathway towards sterols and fatty acids are downregulated. B. The downregulation (panel A) is further supported by the identification of several reporter metabolites of the cholesterol and fatty acid biosynthesis. C. Measurements of cholesterol and triacylglyceride in the plasma. It is seen that the levels of both are down in the mice fed with the herring diet, and this effect is seen both after 8 and 16 weeks of feeding. D. For all downregulated genes identified in the reporter GO terms (panel A) there was searched for enrichment of transcription factors and microRNAs. The heat map shows identified transcription factors and microRNAs and their co-occurrence matrix. It is observed that most regulatory effects are due to a single factor. For some of the identified transcription factors the corresponding consensus binding sites were identified, and this resulted in identification of consensus binding sites for Srebf (Srebp), Hnf4, Pparg and Ppara. The Ppar systems are important lipid-activated nuclear receptors involved in lipid and glucose metabolism; Pparg is an important transcription factor in adipocytes and Ppara in hepatocytes. Hnf4a is an important regulator of coordinated nuclear receptor-mediated response to xenobiotics through interaction with Cars/Pxr and through Hnf1 it activates the expression of a large number of liver-specific genes, including those involved in glucose, cholesterol, and fatty acid metabolism. The most frequent binding site for microRNAs is the site mmu.miR.103 which implies its contribution to transcriptional inhibition of hepatic lipid synthesis (see Text S1and Figure S7).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2927425&req=5

pone-0012361-g003: Mapping of metabolic activities in the liver (green and red indicate down- and upregulated based on herring diet, respectively).A. Overview of genes involved in sterol and lipid biosynthesis that are downregulated in response to herring diet. Besides identification of a key reporter GO terms it is also seen that most genes in the biosynthetic pathway towards sterols and fatty acids are downregulated. B. The downregulation (panel A) is further supported by the identification of several reporter metabolites of the cholesterol and fatty acid biosynthesis. C. Measurements of cholesterol and triacylglyceride in the plasma. It is seen that the levels of both are down in the mice fed with the herring diet, and this effect is seen both after 8 and 16 weeks of feeding. D. For all downregulated genes identified in the reporter GO terms (panel A) there was searched for enrichment of transcription factors and microRNAs. The heat map shows identified transcription factors and microRNAs and their co-occurrence matrix. It is observed that most regulatory effects are due to a single factor. For some of the identified transcription factors the corresponding consensus binding sites were identified, and this resulted in identification of consensus binding sites for Srebf (Srebp), Hnf4, Pparg and Ppara. The Ppar systems are important lipid-activated nuclear receptors involved in lipid and glucose metabolism; Pparg is an important transcription factor in adipocytes and Ppara in hepatocytes. Hnf4a is an important regulator of coordinated nuclear receptor-mediated response to xenobiotics through interaction with Cars/Pxr and through Hnf1 it activates the expression of a large number of liver-specific genes, including those involved in glucose, cholesterol, and fatty acid metabolism. The most frequent binding site for microRNAs is the site mmu.miR.103 which implies its contribution to transcriptional inhibition of hepatic lipid synthesis (see Text S1and Figure S7).
Mentions: In order to identify key biological processes affected by diet in liver, skeletal muscle and WAT, we performed integrated analysis using three biological networks to capture different levels of information. The first analysis provides a global view of the response to diet, identifying significant Gene Ontology (GO)-terms (Figure 2C). We applied the reporter algorithm [4], [14], rather than using the traditional hypogeometric test, since it has the advantage in using the Q-value for all transcripts. The reporter algorithm made it possible to identify key biological processes affected by diet in the three tissues (Figure 2C; for GO “cellular component” and “molecular function” see Figure S4). In liver, the GO biological processes that were affected by diet were related to lipid/sterol metabolism, e.g. “lipid biosynthetic process” (99 transcripts), “sterol biosynthetic process” (25 transcripts) and “cholesterol biosynthetic process” (23 transcripts). Similarly, in muscle and WAT, the GO biological processes affected by diet were translation (321 transcripts, muscle), cell adhesion (419 transcripts, WAT) and defense response to bacterium (77 transcripts, WAT). To further characterize dietary effects on metabolism by the reporter algorithm [4], [14], we also determined key metabolites, using a generic genome-scale metabolic model (GSMM) for mouse [15], and key Reactome processes, using curated evidences from the Reactome database [16]. From this analysis, metabolites related to fatty acid/sterol biosynthesis were identified as the major responses in liver (Figure 3B). Furthermore, specific biological processes related to protein turnover were identified in muscle (Figure 4C). To further identify molecular mechanisms that were triggered by diet, we screened for overrepresentation of regulatory targets, either in the promoter regions or microRNA targets, to identify putative regulatory drivers for the previously identified changes. Hereby, we were able to identify known transcription factors (TFs) and microRNAs that could explain the transcriptional differences in liver and muscle arising from the influence of diet as shown in Figure 3D and Figure S7 (see Text S2 for complete results).

Bottom Line: Changes in lifestyle have resulted in an epidemic development of obesity-related diseases that challenge the healthcare systems worldwide.Our analysis revealed a reduction in sterol metabolism and protein turnover at the transcriptional level in herring-fed mice.This study shows that an integrated analysis of transcriptome data using metabolic networks resulted in the identification of signature pathways.

View Article: PubMed Central - PubMed

Affiliation: Life Sciences/Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.

ABSTRACT

Background: Changes in lifestyle have resulted in an epidemic development of obesity-related diseases that challenge the healthcare systems worldwide. To develop strategies to tackle this problem the focus is on diet to prevent the development of obesity-associated diseases such as cardiovascular disease (CVD). This will require methods for linking nutrient intake with specific metabolic processes in different tissues.

Methodology/principal finding: Low-density lipoprotein receptor-deficient (Ldlr -/-) mice were fed a high fat/high sugar diet to mimic a westernized diet, being a major reason for development of obesity and atherosclerosis. The diets were supplemented with either beef or herring, and matched in macronutrient contents. Body composition, plasma lipids and aortic lesion areas were measured. Transcriptomes of metabolically important tissues, e.g. liver, muscle and adipose tissue were analyzed by an integrated approach with metabolic networks to directly map the metabolic effects of diet in these different tissues. Our analysis revealed a reduction in sterol metabolism and protein turnover at the transcriptional level in herring-fed mice.

Conclusion: This study shows that an integrated analysis of transcriptome data using metabolic networks resulted in the identification of signature pathways. This could not have been achieved using standard clustering methods. In particular, this systems biology analysis could enrich the information content of biomedical or nutritional data where subtle changes in several tissues together affects body metabolism or disease progression. This could be applied to improve diets for subjects exposed to health risks associated with obesity.

Show MeSH
Related in: MedlinePlus