Development of a human mitochondria-focused cDNA microarray (hMitChip) and validation in skeletal muscle cells: implications for pharmaco- and mitogenomics

Alesci, Salvatore; Manoli, Irini; Michopoulos, Vasiliki; Brouwers, Frederieke M.; Le, Hanh; Gold, P W; Blackman, Marc R.; Rennert, Owen M.; Su, Yan; Chrousos, George P.

doi:10.1038/sj.tpj.6500377

Cited by 18 publications

(16 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, the stress responsiveness of these two upstream transcriptional regulatory factors was not differentially regulated by dietary oils, and other factors would contribute to explain the above differences in stress transcriptomics. In this context, it is noteworthy that the modulation of mitochondrial activity by glucocorticoids is considered biphasic with an initial induction of mitochondrial biogenesis and enzymatic activities of selected subunits of the respiratory chain complexes, whereas chronic exposure to high glucocorticoid levels causes respiratory chain dysfunction, increased ROS production, mitochondrial structural abnormalities, apoptosis and cell death (Adzic et al, 2009;Alesci et al, 2006;Manoli et al, 2007). The mechanisms by which GCRs interact with the nuclear and mitochondrial transcription machinery remain largely unknown, especially in fish, though important progress has been made in last years in this field (Aluru and Vijayan, 2009;Schaaf et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

Dietary oils mediate cortisol kinetics and the hepatic mRNA expression profile of stress-responsive genes in gilthead sea bream (Sparus aurata) exposed to crowding stress. Implications on energy homeostasis and stress susceptibility

Pérez‐Sánchez

Borrel

Bermejo-Nogales

et al. 2013

Comparative Biochemistry and Physiology Part D: Genomics and Pr

View full text Add to dashboard Cite

Running title: Nutritional background and stress challenges AbstractJuveniles of gilthead sea bream were fed with plant protein-based diets with fish oil (FO diet) or vegetable oils (66VO diet) as dietary lipid sources. No differences in growth performance were found between both groups, and fish with an average body mass of 65-70 g were crowded (90-100 kg/m 3 ) to assess the stress response within the 72 h after the onset of stressor. The rise in plasma cortisol and glucose levels was higher in stressed fish of group 66VO (66VO-S) than in FO group (FO-S), but the former stressed group regained more quickly the cortisol resting values of the corresponding non-stressed diet group. The cell-tissue repair response represented by derlin-1, 75 kDa glucose-regulated protein and 170 kDa glucose-regulated protein was triggered at a lower level in 66VO-S than in FO-S fish. This occurred in concert with a longlasting up-regulation of glucocorticoid receptors, antioxidant enzymes, enzyme subunits of the mitochondrial respiratory chain, and enzymes involved in tissue fatty acid uptake and β-oxidation. This gene expression pattern allows a metabolic phenotype that is prone to "high 2 power" mitochondria, which would support the replacement of fish oil with vegetables oils when theoretical requirements in essential fatty acids for normal growth are met by diet. IntroductionThe continuous growth of global fish production necessitates less reliance on marine fish meal and fish oil as feed ingredients (Tacon and Metian, 2008; Watanabe, 2002). Table 1). Materials and methods Experimental setupFour hundred and eighty juveniles of gilthead sea bream (Sparus aurata, initial body mass 17 g)were randomly allocated in eight 500-L tanks (60 fish per tank) and reared from May to June (10 weeks) under the natural photoperiod and temperature conditions at our latitude (40°5´N; 0°10´E). Two groups (4 replicates each) were established by feeding fish to visual satiety with plant protein-based diets with either fish oil (FO diet) or a blend of vegetable oils at the 66% of replacement of fish oil (66VO diet) as the most important source of dietary lipids (for details of diet composition see Benedito-Palos et al., 2007). As expected, no effect of diet composition 4 was found on growth or nutrient utilisation and both dietary groups (65-70 g final body mass) had high growth rates (SGR = 1.8-1.9) and good feed:gain ratios (1-1.1).Feeding was stopped one day before crowding challenge start. At that point, three replicates from each dietary group (9-10 kg/m 3 ) remained undisturbed (control fish), whereas the remaining replicate was used as a donor tank of stressed fish, according to the protocol conducted in previous studies (Calduch-Giner et al., 2010;Saera-Vila et al., 2009b) and summarized in Fig. 1. Briefly, for each diet group, seven batches of seven fish from the donor tank were used as stressed fish by transferring all of them at the same time to seven cylinder net baskets of 5-L volume (90-100 kg/m 3 ), each one suspended in 90-L tanks w...

show abstract

Section: Discussionmentioning

confidence: 99%

Dietary oils mediate cortisol kinetics and the hepatic mRNA expression profile of stress-responsive genes in gilthead sea bream (Sparus aurata) exposed to crowding stress. Implications on energy homeostasis and stress susceptibility

Pérez‐Sánchez

Borrel

Bermejo-Nogales

et al. 2013

Comparative Biochemistry and Physiology Part D: Genomics and Pr

View full text Add to dashboard Cite

show abstract

“…Two days after induction of differentiation, cells were incubated with 100 µM DEX for 4 days to induce atrophy. [44][45][46][47] Six days after the induction of differentiation, we took photos at three random spots in each group. For observing atrophy, we measured fusion index and myotube area.…”

Section: Induction Of Atrophymentioning

confidence: 99%

Schisandrae fructus enhances myogenic differentiation and inhibits atrophy through protein synthesis in human myotubes

Kim

Shin

Hwang

et al. 2016

IJN

View full text Add to dashboard Cite

Schisandrae fructus (SF) has recently been reported to increase skeletal muscle mass and inhibit atrophy in mice. We investigated the effect of SF extract on human myotube differentiation and its acting pathway. Various concentrations (0.1–10 μg/mL) of SF extract were applied on human skeletal muscle cells in vitro. Myotube area and fusion index were measured to quantify myotube differentiation. The maximum effect was observed at 0.5 μg/mL of SF extract, enhancing differentiation up to 1.4-fold in fusion index and 1.6-fold in myotube area at 8 days after induction of differentiation compared to control. Phosphorylation of eukaryotic translation initiation factor 4E-binding protein 1 and 70 kDa ribosomal protein S6 kinase, which initiate translation as downstream of mammalian target of rapamycin pathway, was upregulated in early phases of differentiation after SF treatment. SF also attenuated dexamethasone-induced atrophy. In conclusion, we show that SF augments myogenic differentiation and attenuates atrophy by increasing protein synthesis through mammalian target of rapamycin/70 kDa ribosomal protein S6 kinase and eukaryotic translation initiation factor 4E-binding protein 1 signaling pathway in human myotubes. SF can be a useful natural dietary supplement in increasing skeletal muscle mass, especially in the aged with sarcopenia and the patients with disuse atrophy.

show abstract

“…Test genes (1135), 146 positive controls (housekeeping and duplicate genes), and 79 negative controls (print-buffer without DNA) were printed in triplicate onto each hMitChip3 slide (see Supplementary Table S1) as previously described (18), using the OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA). Spike-in DNA controls for possible contamination (plasmid DNA), blocking efficiency (salmon sperm DNA), and cross-hybridization (human Cot-1 repetitive DNA), previously included in hMitChip2, were not necessarily repeated here (14,15). …”

Section: Methodsmentioning

confidence: 99%

“…In addition, the National Center for Biotechnology Information (NCBI) and other public databases were searched using keywords mitochondrial biogenesis and oxidative stress as previously described (14). Transcriptional loci predicted from sequences were not included.…”

Section: Methodsmentioning

confidence: 99%

“…To provide such a tool, we previously developed a first-generation human mitochondrial-focused cDNA microarray (hMitChip1, unpublished) and a second-generation human mitochondrial-focused cDNA microarray (hMitChip2) (14). hMitChip2, which contained only 501 nuclear DNA-encoded genes, was tested and validated in human skeletal muscle cells in an attempt to better understand mitochondrial involvement in glucocorticoid-induced myopathy (15).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Third-Generation Human Mitochondria-Focused cDNA Microarray and Its Bioinformatic Tools for Analysis of Gene Expression

Bai

Jun²,

Zhang³

et al. 2007

BioTechniques

View full text Add to dashboard Cite

To facilitate profiling mitochondrial transcriptomes, we developed a third-generation human mitochondria-focused cDNA microarray (hMitChip3) and its bioinformatic tools. hMitChip3 consists of the 37 mitochondrial DNA-encoded genes, 1098 nuclear DNA-encoded and mitochondria-related genes, and 225 controls, each in triplicate. The bioinformatic tools included data analysis procedures and customized database for interpretation of results. The database associated 645 molecular functions with 946 hMitChip3 genes, 612 biological processes with 930 genes, 172 cellular components with 869 genes, 107 biological chemistry pathways with 476 genes, 23 reactome events with 227 genes, 320 genetic disorders with 237 genes, and 87 drugs targets with 55 genes. To test these tools, hMitChip3 was used to compare expression profiles between human melanoma cell lines UACC903 (rapidly dividing) and UACC903(+6) (slowly dividing). Our results demonstrated internal gene-set consistency (correlation R > or = 0.980 +/- 0.005) and interexperimental reproducibility (R > or = 0.931 +/- 0.013). Expression patterns of 16 genes, involved in DNA, RNA, or protein biosyntheses in mitochondrial and other organelles, were consistent with the proliferation rates of both cell lines, and the patterns of 6 tested genes were verified by quantitative reverse transcription PCR (RT-PCR). Thus, hMitChip3 and its bioinformatics software provide an integrated tool for profiling mitochondria-focused gene expression.

show abstract

Development of a human mitochondria-focused cDNA microarray (hMitChip) and validation in skeletal muscle cells: implications for pharmaco- and mitogenomics

Cited by 18 publications

References 63 publications

Dietary oils mediate cortisol kinetics and the hepatic mRNA expression profile of stress-responsive genes in gilthead sea bream (Sparus aurata) exposed to crowding stress. Implications on energy homeostasis and stress susceptibility

Dietary oils mediate cortisol kinetics and the hepatic mRNA expression profile of stress-responsive genes in gilthead sea bream (Sparus aurata) exposed to crowding stress. Implications on energy homeostasis and stress susceptibility

Schisandrae fructus enhances myogenic differentiation and inhibits atrophy through protein synthesis in human myotubes

Third-Generation Human Mitochondria-Focused cDNA Microarray and Its Bioinformatic Tools for Analysis of Gene Expression

Contact Info

Product

Resources

About