Short chain acyl-CoA dehydrogenase deficiency and short-term high-fat diet perturb mitochondrial energy metabolism and transcriptional control of lipid-handling in liver

Ghosh, Sujoy; Krüger, Claudia; Wicks, Shawna E.; Simon, Jacob; Kumar, K. Ganesh; Johnson, William D.; Mynatt, Randall L.; Noland, Robert C.; Richards, Brenda

doi:10.1186/s12986-016-0075-0

Cited by 15 publications

(11 citation statements)

References 46 publications

(62 reference statements)

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“…Mice were acclimated to constant dark for 6 weeks, and livers were harvested at 9:00 am (CT1), and then every 4 h, (CT5, CT9, CT13, CT17, and CT21) for 6 time-points. RNA-Seq data was presented as reads count of pooled samples [39]. For these selected genes, RT-qPCR verified their rhythms and confirmed the MetaCycle results.…”

Section: Discussionsupporting

confidence: 56%

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Endogenous circadian time genes expressions in the liver of mice under constant darkness

Zhang

et al. 2020

BMC Genomics

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Background: The circadian rhythms regulate physiological functions and metabolism. Circadian Time (CT) is a unit to quantify the rhythm of endogenous circadian clock, independent of light influence. To understand the gene expression changes throughout CT, C57BL/6 J mice were maintained under constant darkness (DD) for 6 weeks, and the liver samples were collected starting at 9:00 AM (CT1), and every 4 h in a 24-h cycle (CT5, CT9, CT13, CT17 and CT21). Total RNA was extracted and subjected to RNA-Seq data (deposited as GSE 133342, L-DD). To compare gene oscillation pattern under normal light-dark condition (LD, GSE114400) and short time (2 days) dark-dark condition (S-DD, GSE70497), these data were retried from GEO database, and the trimmed mean of M-values normalization was used to normalize the three RNA-seq data followed by MetaCycle analysis. Results: Approximate 12.1% of the genes under L-DD exhibited significant rhythmically expression. The top 5 biological processes enriched in L-DD oscillation genes were mRNA processing, aromatic compound catabolic process, mitochondrion organization, heterocycle catabolic process and cellular nitrogen compound mitotic catabolic process. The endogenous circadian rhythms of clock genes, P450 genes and lipid metabolism genes under L-DD were further compared with LD and S-DD. The oscillation patterns were similar but the period and amplitude of those oscillation genes were slightly altered. RT-qPCR confirmed the selected RNA sequence findings. Conclusions: This is the first study to profile oscillation gene expressions under L-DD. Our data indicate that clock genes, P450 genes and lipid metabolism genes expressed rhythmically under L-DD. Light was not the necessary factor for persisting circadian rhythm but influenced the period and amplitude of oscillation genes.

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Section: Discussionsupporting

confidence: 56%

“…On the contrary, the periods of Lipin1 and Lipin2 were increased under L-DD. Stearoyl-Coenzyme A desaturase (Scd) genes encode the key enzymes involved in the conversion of saturated fatty acids into monounsaturated fatty acids [39]. L-DD decreased the period of Scd1 and Scd2.…”

Section: Resultsmentioning

confidence: 99%

Endogenous circadian time genes expressions in the liver of mice under constant darkness

Zhang

et al. 2020

BMC Genomics

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“…Several genes that are cis -regulated in the muscle participate in lipid or carbohydrate metabolism, e.g. HIV-1 Tat Interactive Protein 2 ( HTATIP2 ) [14], exocyst complex component 7 ( EXOC7 ) [15] acyl-CoA dehydrogenase short chain ( ACADS ) [16], insulin degrading enzyme ( IDE ) [17], solute carrier family 38 member 9 ( SLC38A9 ) [18], and family with sequence similarity 3 member C ( FAM3C ) [19]. With regard to the liver, hydroxysteroid dehydrogenase like 2 ( HSDL2 ) [20] and lipase A ( LIPA ) [21] genes have also important roles in lipid metabolism.…”

Section: Resultsmentioning

confidence: 99%

About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

et al. 2019

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Background The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we have compared the transcriptomic and eQTL profiles of two porcine tissues (skeletal muscle and liver) which typically show highly divergent expression profiles, in 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray-based measurements of hepatic and muscle mRNA levels. Since structural variation could have effects on gene expression, we have also investigated the co-localization of cis- eQTLs with copy number variant regions (CNVR) segregating in this Duroc population. Results The analysis of differential expresssion revealed the existence of 1204 and 1490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value < 0.05). By performing genome scans in 103 Duroc pigs with available expression and genotypic data, we identified 76 and 28 genome-wide significant cis- eQTLs regulating gene expression in the gluteus medius muscle and liver, respectively. Twelve of these cis -eQTLs were shared by both tissues (i.e. 42.8% of the cis- eQTLs identified in the liver were replicated in the gluteus medius muscle). These results are consistent with previous studies performed in humans, where 50% of eQTLs were shared across tissues. Moreover, we have identified 41 CNVRs in a set of 350 pigs from the same Duroc population, which had been genotyped with the Porcine SNP60 BeadChip by using the PennCNV and GADA softwares, but only a small proportion of these CNVRs co-localized with the cis -eQTL signals. Conclusion Despite the fact that there are considerable differences in the gene expression patterns of the porcine liver and skeletal muscle, we have identified a substantial proportion of common cis- eQTLs regulating gene expression in both tissues. Several of these cis -eQTLs influence the mRNA levels of genes with important roles in meat ( CTSF ) and carcass quality ( TAPT1 ), lipid metabolism ( TMEM97 ) and obesity ( MARC2 ), thus evidencing the practical importance of dissecting the genetic mechanisms involved in their expression. Electronic supplementary material The online version of this article (10.1186/s12864-019-5889-5) contains supplementary material, which is available to authorized users.

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“…Studies have shown that macrophage activation stimulated by LPS promotes an increase in glucose uptake and glycolysis, giving preference to this pathway to supply the energy demand of pro-inflammatory processes 44 . Fatty acids degradation was also overrepresented for turquoise module, and this is an important energy production pathway, especially for tissues that have a high metabolic demand, such as the liver, the main organ for homeostasis regulation in mammals 45 . Fatty acids are released from adipose tissue and absorbed by hepatocytes where they will be oxidized to ATP production, which will act as energy source or converted into lipid molecules and derivatives 46 .…”

Section: Discussionmentioning

confidence: 99%

Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle

Fonseca

Eler

Pereira

et al. 2019

Sci Rep

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Improving nutrient utilization efficiency is essential for livestock, given the current scenario of increasing demand for animal protein and sustainable resource use. In this context, understanding the biology of feed efficiency (FE) in beef cattle allows the development of markers for identification and selection of best animals for animal production. Thus, 98 young Nellore bulls were evaluated for FE and at the end of the experiment liver samples from six High Feed Efficient (HFE) and six Low Feed Efficient (LFE) animals were collected for protein extraction, digestion and analysis by HPLC-MS/MS. Data were analyzed for differential abundant proteins (DAPs), protein networks, and functional enrichment. Serum endotoxin was also quantified. We found 42 DAPs and 3 protein networks significantly related to FE. The main pathways associated with FE were: microbial metabolism; biosynthesis of fatty acids, amino acids and vitamins; glycolysis/gluconeogenesis; xenobiotic metabolism and; antigen processing and presentation. Serum endotoxins were significantly higher in LFE animals supporting the results. Therefore, the findings presented here confirmed the altered hepatic metabolism and pronounced hepatic inflammation in LFE animals supporting that the increased bacterial load is at least in part responsible for the hepatic lesions and inflammation in LFE animals.

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Short chain acyl-CoA dehydrogenase deficiency and short-term high-fat diet perturb mitochondrial energy metabolism and transcriptional control of lipid-handling in liver

Cited by 15 publications

References 46 publications

Endogenous circadian time genes expressions in the liver of mice under constant darkness

Endogenous circadian time genes expressions in the liver of mice under constant darkness

About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle

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