Genomic analysis of metabolic pathway gene expression in mice.
Ontology highlight
ABSTRACT: Background
A segregating population of (C57BL/6J x DBA/2J)F2 intercross mice was studied for obesity-related traits and for global gene expression in liver. Quantitative trait locus analyses were applied to the subcutaneous fat-mass trait and all gene-expression data. These data were then used to identify gene sets that are differentially perturbed in lean and obese mice.Results
We integrated global gene-expression data with phenotypic and genetic segregation analyses to evaluate metabolic pathways associated with obesity. Using two approaches we identified 13 metabolic pathways whose genes are coordinately regulated in association with obesity. Four genomic regions on chromosomes 3, 6, 16, and 19 were found to control the coordinated expression of these pathways. Using criteria that included trait correlation, differential gene expression, and linkage to genomic regions, we identified novel genes potentially associated with the identified pathways.Conclusion
This study demonstrates that genetic and gene-expression data can be integrated to identify pathways associated with clinical traits and their underlying genetic determinants.
SUBMITTER: Ghazalpour A
PROVIDER: S-EPMC1175990 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Celeribacter indicus P73(T), isolated from deep-sea sediment from the Indian Ocean, is capable of degrading a wide range of polycyclic aromatic hydrocarbons (PAHs) and is the first fluoranthene-degrading bacterium within the family Rhodobacteraceae. Here, the complete genome sequence of strain P73(T) is presented and analyzed. Besides a 4.5-Mb circular chromosome, strain P73(T) carries five plasmids, and encodes 4827 predicted protein-coding sequences. One hundred and thirty-eight genes, including 14 dioxygenase genes, were predicted to be involved in the degradation of aromatic compounds, and most of these genes are clustered in four regions. P73_0346 is the first fluoranthene 7,8-dioxygenase to be discovered and the first fluoranthene dioxygenase within the toluene/biphenyl family. The degradative genes in regions B and D in P73(T) are absent in Celeribacter baekdonensis B30, which cannot degrade PAHs. Four intermediate metabolites [acenaphthylene-1(2H)-one, acenaphthenequinone, 1,2-dihydroxyacenaphthylene, and 1,8-naphthalic anhydride] of fluoranthene degradation by strain P73(T) were detected as the main intermediates, indicating that the degradation of fluoranthene in P73(T) was initiated by dioxygenation at the C-7,8 positions. Based on the genomic and metabolitic results, we propose a C-7,8 dioxygenation pathway in which fluoranthene is mineralized to TCA cycle intermediates.
| S-EPMC4291564 | biostudies-literature
Project description:In Arabidopsis thaliana, blocking histidine biosynthesis with a specific inhibitor of imidazoleglycerol-phosphate dehydratase caused increased expression of eight genes involved in the biosynthesis of aromatic amino acids, histidine, lysine, and purines. A decrease in expression of glutamine synthetase was also observed. Addition of histidine eliminated the gene-regulating effects of the inhibitor, demonstrating that the changes in gene expression resulted from histidine-pathway blockage. These results show that plants are capable of cross-pathway metabolic regulation.
| S-EPMC41834 | biostudies-other
Project description:Copy number variants (CNVs) are genomic segments which are duplicated or deleted among different individuals. CNVs have been implicated in both Mendelian and complex traits, including immune and behavioral disorders, but the study of the mechanisms by which CNVs influence gene expression and clinical phenotypes in humans is complicated by the limited access to tissues and by population heterogeneity. We now report studies of the effect of 19 CNVs on gene expression and metabolic traits in a mouse intercross between strains C57BL/6J and C3H/HeJ. We found that 83% of genes predicted to occur within CNVs were differentially expressed. The expression of most CNV genes was correlated with copy number, but we also observed evidence that gene expression was altered in genes flanking CNVs, suggesting that CNVs may contain regulatory elements for these genes. Several CNVs mapped to hotspots, genomic regions influencing expression of tens or hundreds of genes. Several metabolic traits including cholesterol, triglycerides, glucose and body weight mapped to three CNVs in the genome, in mouse chromosomes 1, 4 and 17. Predicted CNV genes, such as Itlna, Defcr-1, Trim12 and Trim34 were highly correlated with these traits. Our results suggest that CNVs have a significant impact on gene expression and that CNVs may be playing a role in the mechanisms underlying metabolic traits in mice.
| S-EPMC2758141 | biostudies-literature
Project description:Icariin is effective in the treatment of hyperlipidemia. To understand the effect of icariin on lipid metabolism, effects of icariin on PPAR? and its target genes were investigated. Mice were treated orally with icariin at doses of 0, 100, 200, and 400 mg/kg, or clofibrate (500 mg/kg) for five days. Liver total RNA was isolated and the expressions of PPAR? and lipid metabolism genes were examined. PPAR? and its marker genes Cyp4a10 and Cyp4a14 were induced 2-4 fold by icariin, and 4-8 fold by clofibrate. The fatty acid (FA) binding and co-activator proteins Fabp1, Fabp4 and Acsl1 were increased 2-fold. The mRNAs of mitochondrial FA ?-oxidation enzymes (Cpt1a, Acat1, Acad1 and Hmgcs2) were increased 2-3 fold. The mRNAs of proximal ?-oxidation enzymes (Acox1, Ech1, and Ehhadh) were also increased by icariin and clofibrate. The expression of mRNAs for sterol regulatory element-binding factor-1 (Srebf1) and FA synthetase (Fasn) were unaltered by icariin. The lipid lysis genes Lipe and Pnpla2 were increased by icariin and clofibrate. These results indicate that icariin is a novel PPAR? agonist, activates lipid metabolism gene expressions in liver, which could be a basis for its lipid-lowering effects and its beneficial effects against diabetes.
| S-EPMC6270773 | biostudies-literature
Project description:Island populations repeatedly evolve extreme body sizes, but the genomic basis of this pattern remains largely unknown. To understand how organisms on islands evolve gigantism, we compared genome-wide patterns of gene expression in Gough Island mice, the largest wild house mice in the world, and mainland mice from the WSB/EiJ wild-derived inbred strain. We used RNA-seq to quantify differential gene expression in three key metabolic organs: gonadal adipose depot, hypothalamus, and liver. Between 4,000 and 8,800 genes were significantly differentially expressed across the evaluated organs, representing between 20% and 50% of detected transcripts, with 20% or more of differentially expressed transcripts in each organ exhibiting expression fold changes of at least 2×. A minimum of 73 candidate genes for extreme size evolution, including Irs1 and Lrp1, were identified by considering differential expression jointly with other data sets: 1) genomic positions of published quantitative trait loci for body weight and growth rate, 2) whole-genome sequencing of 16 wild-caught Gough Island mice that revealed fixed single-nucleotide differences between the strains, and 3) publicly available tissue-specific regulatory elements. Additionally, patterns of differential expression across three time points in the liver revealed that Arid5b potentially regulates hundreds of genes. Functional enrichment analyses pointed to cell cycling, mitochondrial function, signaling pathways, inflammatory response, and nutrient metabolism as potential causes of weight accumulation in Gough Island mice. Collectively, our results indicate that extensive gene regulatory evolution in metabolic organs accompanied the rapid evolution of gigantism during the short time house mice have inhabited Gough Island.
| S-EPMC7487164 | biostudies-literature
Project description:Gene expression and Comparative genomic hybridization (CGH) microarrays performed in a set of 8 Lung cancer Cell lines. The search for oncogenes is becoming increasingly important in cancer genetics because they constitute suitable targets for therapeutic intervention. To identify novel oncogenes, activated by gene amplification, we performed high-resolution CGH (Comparative Genome Hybridization) analysis on cDNA microarrays and compared DNA copy number and mRNA expression levels in lung cancer cell lines. We have performed both microarrays (expression and CGH) in a set of 8 human lung cancer cell lines: Calu3, H23, H441, A427, H522, A549, H1299, H2126.
| S-ECPF-GEOD-14079 | biostudies-other
Project description:Background/Aim: Angiotensin II (Ang II) and hypertension play critical roles in the pathogenesis of the atrial remodeling that contributes to atrial fibrillation (AF). However, the gene expression profiles and signaling pathways in atria during the development of AF induced by Ang II remain unknown. Methods: Wild-type male mice (C57BL/6 background, 10 weeks old) were administered an infusion of Ang II (2000 ng/kg/min) using an osmotic pump for 1, 2, and 3 weeks. Blood pressure (BP) was measured by the tail-cuff method. AF was induced and recorded. Atrial enlargement and remodeling were examined by echocardiography and Masson's trichrome staining. Time-series microarray analyses were conducted to examine gene expression profiles and pathways. Results: Ang II infusion resulted in marked elevation of systolic BP, increased AF incidence and duration, atrial enlargement, fibrosis, and atrial infiltration of myofibroblasts and F4/80-positive macrophages in a time-dependent manner. Microarray results showed that 1,719 genes were differentially expressed in the atrium at weeks 1, 2, and 3 after Ang II infusion. Gene ontology showed that these genes participate mainly in immune system processes, and regulation of cell migration, cell adhesion, complement activation, and the inflammatory response. Significant pathways included lysosomal and phagosomal pathways, which are involved in antigen processing and presentation, as well as chemokine signaling, and extracellular matrix-receptor interaction, which are known to play important roles in Ang II-induced AF. Moreover, these differentially expressed genes were classified into 50 profiles by hierarchical cluster analysis. Of these, eight profiles were significant and contained a total of 1,157 genes. Gene co-expression network analysis identified that Pik3cg (also known as phosphoinositide-3-kinase regulatory subunit 3) was localized in the core of the gene network, and was the most highly expressed among the Pik3 isoforms at different time points. Conclusion: The present findings revealed that many genes are involved in Ang II-induced AF, and highlighted that Pik3cg may play a central role in this disease.
| S-EPMC6548816 | biostudies-literature
Project description:The metabolic adaptation of dairy cows during the transition period has been studied intensively in the last decades. However, until now, only few studies have paid attention to the genetic aspects of this process. Here, we present the results of a gene-based mapping and pathway analysis with the measurements of three key metabolites, (1) non-esterified fatty acids (NEFA), (2) beta-hydroxybutyrate (BHBA) and (3) glucose, characterizing the metabolic adaptability of dairy cows before and after calving. In contrast to the conventional single-marker approach, we identify 99 significant and biologically sensible genes associated with at least one of the considered phenotypes and thus giving evidence for a genetic basis of the metabolic adaptability. Moreover, our results strongly suggest three pathways involved in the metabolism of steroids and lipids are potential candidates for the adaptive regulation of dairy cows in their early lactation. From our perspective, a closer investigation of our findings will lead to a step forward in understanding the variability in the metabolic adaptability of dairy cows in their early lactation.
| S-EPMC4366076 | biostudies-literature
Project description:Adenosine is an endogenous molecule that regulates many physiological processes via the activation of four specific G-protein-coupled ADORA receptors. Extracellular adenosine may originate either from the hydrolysis of released ATP by the ectonucleotidases or from cellular exit via the equilibrative nucleoside transporters (SLC29A). Adenosine extracellular concentration is also regulated by its successive hydrolysis into uric acid by membrane-bound enzymes or by cell influx via the concentrative nucleoside transporters (SLC28A). All of these members constitute the adenosine signaling pathway and regulate adenosine functions. Although the roles of this pathway are quite well understood in adults, little is known regarding its functions during vertebrate embryogenesis. We have used Xenopus laevis as a model system to provide a comparative expression map of the different members of this pathway during vertebrate development. We report the characterization of the different enzymes, receptors, and nucleoside transporters in both X. laevis and X. tropicalis, and we demonstrate by phylogenetic analyses the high level of conservation of these members between amphibians and mammals. A thorough expression analysis of these members during development and in the adult frog reveals that each member displays distinct specific expression patterns. These data suggest potentially different developmental roles for these proteins and therefore for extracellular adenosine. In addition, we show that adenosine levels during amphibian embryogenesis are very low, confirming that they must be tightly controlled for normal development.
| S-EPMC4336307 | biostudies-literature
Project description:Since the first report that Stxbp6, a brain-enriched protein, regulates the assembly of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes, little has been discovered about its functions over the past two decades. To determine the effects of Stxbp6 loss on nervous-system-associated phenotypes and underlying mechanisms, we constructed a global Stxbp6-knockout mouse. We found that Stxbp6-null mice survive normally, with normal behavior, but gained less weight relative to age- and sex-matched wildtype mice. RNA-seq analysis of the cerebral cortex of Stxbp6-null mice relative to wildtype controls identified 126 differentially expressed genes. Of these, 57 were upregulated and 69 were downregulated. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the most significant enriched KEGG term was "complement and coagulation cascades". Our results suggest some potential regulatory pathways of Stxbp6 in the central nervous system, providing a remarkable new resource for understanding Stxbp6 function at the organism level.
| S-EPMC8066043 | biostudies-literature