Identifying critical genes and pathways of doxorubicin-induced cardiomyopathy via bioinformatics analysis

OBJECTIVE

The pathogenesis of doxorubicin (DOX) induced cardiomyopathy (DCM) is still uncertain. We aimed to identify the critical genes and pathways involved in DCM based on bioinformatics analysis.

MATERIALS AND METHODS

The GSE59672 and GSE23598 mice heart tissue microarray data were obtained from Gene Expression Omnibus (GEO) database. The "limma" package of R software was used to screen the differently expressed genes (DEGs). GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses were performed on DEGs by using "clusterProfiler" package in R software. The PPI (Protein - Protein Interaction) network of DEGs constructed by STRING online database and thereby the top 15 hub genes selected by cytoHubba in Cytoscape software. The hub genes interaction was performed by GeneMANIA online database. The "Corrplot" R package was employed to assess hub genes correlation.

RESULTS

Finally, a total of 492 and 501 DEGs were screened in GSE59672 and GSE23598 datasets, respectively. GO analyses revealed that DEGs were mainly involved in the regulation of extracellular matrix organization, metabolic process, regulation of collagen-containing extracellular matrix. KEGG pathway analyses indicated that DEGs were mainly involved in protein digestion and absorption, ECM-receptor interaction, phagosome, and p53 signaling pathway. Finally, the 8 hub genes were identified, including Col1a1, Col3a1, Col1a2, Col6a1, Ptprc, Tyrobp, Itgb2, and Ctss.

CONCLUSIONS

The present study identified a series of key genes, including Col1a1, Col3a1, Col1a2, Col6a1, Ptprc, Tyrobp, Itgb2, and Ctss. In addition, important pathways were also discovered. The results of this study may provide a novel molecular mechanism and potential therapeutic targets for DCM.

Fertilization- and Irrigation-Modified Bacterial Community Composition and Stimulated Enzyme Activity of Eucalyptus Plantations Soil

Irrigation and fertilization are essential management practices for increasing forest productivity. They also impact the soil ecosystem and the microbial population. In order to examine the soil bacterial community composition and structure in response to irrigation and fertilization in a Eucalyptus plantations, a total of 20 soil samples collected from Eucalyptus plantations were analyzed using high-throughput sequencing. Experimental treatments consisting of control (CK, no irrigation or fertilization), fertilization only (F), irrigation only (W), and irrigation and fertilization (WF). The results showed a positive correlation between soil enzyme activities (urease, cellulase, and chitinase) and fertilization treatments. These enzyme activities were also significantly correlated with the diversity of soil bacterial communities in Eucalyptus plantations.. Bacteria diversity was considerably increased under irrigation and fertilization (W, F, and WF) treatments when compared with the CK treatment. Additionally, the soil bacterial richness was increased in the Eucalyptus plantations soil under irrigation (W and WF) treatments. The Acidobacteria (38.92-47.9%), Proteobacteria (20.50-28.30%), and Chloroflexi (13.88-15.55%) were the predominant phyla found in the Eucalyptus plantations soil. Specifically, compared to the CK treatment, the relative abundance of Proteobacteria was considerably higher under the W, F, and WF treatments, while the relative abundance of Acidobacteria was considerably lower. The contents of total phosphorus, accessible potassium, and organic carbon in the soil were all positively associated with fertilization and irrigation treatments. Under the WF treatment, the abundance of bacteria associated with nitrogen and carbon metabolisms, enzyme activity, and soil nutrient contents showed an increase, indicating the positive impact of irrigation and fertilization on Eucalyptus plantations production. Collectively, these findings provide the scientific and managerial bases for improving the productivity of Eucalyptus plantations.

Optimized wake-superposition approach for multiturbine wind farms

Optimizing the wind farm layout requires accurately quantifying the wind-turbine wake distribution to minimize interference between wakes. Thus, the accuracy of wind turbine wake superposition models is critical. The sum of squares (SS) model is currently touted as the most accurate, but its application in engineering is hampered by its overestimation of the velocity deficit of the mixed wake. Therefore, previous work relied on approximate power calculations for performing optimization. The physical meaning of the SS model is unclear, which makes optimization difficult. In this study, a univariate linear correction idea is proposed based on the linear increase phenomenon of the SS method error. The unknown coefficients are obtained by fitting experimental data. The results demonstrate that the proposed method can accurately quantify the full-wake two-dimensional distribution of the mixed wake.

The CRTC-CREB axis functions as a transcriptional sensor to protect against proteotoxic stress in Drosophila

cAMP Responsible Element Binding Protein (CREB) is an evolutionarily conserved transcriptional factor that regulates cell growth, synaptic plasticity and so on. In this study, we unexpectedly found proteasome inhibitors, such as MLN2238, robustly increase CREB activity in adult flies through a large-scale compound screening. Mechanistically, reactive oxidative species (ROS) generated by proteasome inhibition are required and sufficient to promote CREB activity through c-Jun N-terminal kinase (JNK). In 293 T cells, JNK activation by MLN2238 is also required for increase of CREB phosphorylation at Ser¹³³. Meanwhile, transcriptome analysis in fly intestine identified a group of genes involved in redox and proteostatic regulation are augmented by overexpressing CRTC (CREB-regulated transcriptional coactivator). Intriguingly, CRTC overexpression in muscles robustly restores protein folding and proteasomal activity in a fly Huntington's disease (HD) model, and ameliorates HD related pathogenesis, such as protein aggregates, motility, and lifespan. Moreover, CREB activity increases during aging, and further enhances its activity can suppress protein aggregates in aged muscles. Together, our results identified CRTC/CREB downstream ROS/JNK signaling as a conserved sensor to tackle oxidative and proteotoxic stresses. Boosting CRTC/CREB activity is a potential therapeutic strategy to treat aging related protein aggregation diseases.

Mifepristone (RU486) inhibits dietary lipid digestion by antagonizing the role of glucocorticoid receptor on lipase transcription

Lipid digestion and absorption are tightly regulated to cope with metabolic demands among tissues. How these processes are coordinated is not well characterized. Here, we found that mifepristone (RU486) prevents lipid digestion both in flies and mice. In flies, RU486 administration suppresses lipid digestion by transcriptional downregulating Magro in guts. Similarly, intestinal lipid uptake in mice was also suppressed by RU486 through the glucocorticoid receptor (GR). Further studies showed that the pancreatic lipase Pnlip is a direct transcriptional target of GR in pancreas tissues. Glucocorticoid levels in mice fed a high fat diet (HFD) are significantly lower than those fed on a conventional diet, and RU486 administration inhibits HFD-induced obesity both in mice and flies. Our findings identified a novel mechanism of RU486 functions as a GR antagonist systematically regulating lipid metabolism, providing new insight on the role of Glucocorticoid/GR in Cushing disease, diabetes, and other related metabolic syndromes.

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RU486 suppresses lipid digestion both in mice and flies.

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In flies, lipase Magro is transcriptionally suppressed by RU486 through dERR.

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In mice, intestinal lipid digestion is inhibited by RU486 through (GR)/PTL pathway in pancreas.

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RU486 alleviates high fat diet-induced obesity both in flies and mice.

Effect of Protein Supplementation Combined with Resistance Training on Muscle Mass, Strength and Function in the Elderly: A Systematic Review and Meta-Analysis

BACKGROUND

The loss of muscle mass, strength and function associated with increasing age has various health ramifications, including the elevated risk for falls, fractures, frailty, poor quality of life, and mortality. Several studies have confirmed the effects of protein supplementation and RT (resistance training) for this age-related change independently, but whether a combination of the two produces a stronger effect remains controversial.

OBJECTIVE

This study aims to explore whether a combination of protein supplementation and RT leads to reduction of muscle mass, strength and function in the elderly.

METHODS

We retrieved RCTs (randomized controlled trials) reporting the effects of protein supplementation combined with RT on muscle mass, strength and function in the elderly, published before May 2018 through PubMed, MEDLINE, Embase, and manual searches.

RESULTS

Twenty-one RCTs were included, involving 1,249 participants. The results showed that protein supplementation combine with RT significantly enhances the muscle mass and strength of the older adults, where FFM (fat-free mass) increased by 0.23 kg (95% CI: 0.09, 0.38; P=0.002), ASMM (appendicular skeletal muscle mass) by 0.39 kg (95% CI: 0.14, 0.64; P=0.002), handgrip strength by 0.29 kg (95% CI: 0.08, 0.50; P=0.008), knee extension strength by 0.27 kg (95% CI: 0.06, 0.47; P=0.013), leg press strength by 0.33 kg (95% CI: 0.01, 0.64; P=0.04), but no significant effects were seen on muscle function.

CONCLUSION

Compared to simple RT, protein supplementation combine with RT is more effective in enhancing the muscle mass and strength in the elderly, and the findings do not support the benefit of combination treatment for muscle function.

Green tea polyphenols as a natural tumour cell proteasome inhibitor

The cancer-preventive effects of green tea and its main constituent (-)-epigallocatechin gallate [(-)-EGCG] are widely supported by results from epidemiological, cell culture, animal and clinical studies although the molecular target has not been well defined. We previously reported that ester bond-containing tea polyphenols, e. g. (-)-EGCG, and their synthetic analogs potently and specifically inhibited the proteasomal activity. Subsequently, we further demonstrated that methylation on green tea polyphenols under physiological conditions decreased their proteasome-inhibitory activity, contributing to decreased cancer-preventive effects of tea consumption. Since (-)-EGCG is unstable under physiological conditions, we also developed the peracetate-protected or prodrug form of (-)-EGCG, Pro-EGCG (1), and shown that Pro-EGCG (1) increases the bioavailability, stability, and proteasome-inhibitory and anticancer activities of (-)-EGCG in human breast cancer cells and xenografts, suggesting its potential use for cancer prevention and treatment.

Tea polyphenols, their biological effects and potential molecular targets

Tea is the most popular beverage in the world, second only to water. Tea contains an infusion of the leaves from the Camellia sinensis plant rich in polyphenolic compounds known as catechins, the most abundant of which is (-)-EGCG. Although tea has been consumed for centuries, it has only recently been studied extensively as a health-promoting beverage that may act to prevent a number of chronic diseases and cancers. The results of several investigations indicate that green tea consumption may be of modest benefit in reducing the plasma concentration of cholesterol and preventing atherosclerosis. Additionally, the cancer-preventive effects of green tea are widely supported by results from epidemiological, cell culture, animal and clinical studies. In vitro cell culture studies show that tea polyphenols potently induce apoptotic cell death and cell cycle arrest in tumor cells but not in their normal cell counterparts. Green tea polyphenols were shown to affect several biological pathways, including growth factor-mediated pathway, the mitogen-activated protein (MAP) kinase-dependent pathway, and ubiquitin/proteasome degradation pathways. Various animal studies have revealed that treatment with green tea inhibits tumor incidence and multiplicity in different organ sites such as skin, lung, liver, stomach, mammary gland and colon. Recently, phase I and II clinical trials have been conducted to explore the anticancer effects of green tea in humans. A major challenge of cancer prevention is to integrate new molecular findings into clinical practice. Therefore, identification of more molecular targets and biomarkers for tea polyphenols is essential for improving the design of green tea trials and will greatly assist in a better understanding of the mechanisms underlying its anti-cancer activity.

Theoretical and empirical scaling patterns and topological homology in bone trabeculae

Trabecular or cancellous bone is a major element in the structural design of the vertebrate skeleton, but has received little attention from the perspective of the biology of scale. In this study, we investigated scaling patterns in the discrete bony elements of cancellous bone. First, we constructed two theoretical models, representative of the two extremes of realistic patterns of trabecular size changes associated with body size changes. In one, constant trabecular size (CTS), increases in cancellous bone volume with size arise through the addition of new elements of constant size. In the other model, constant trabecular geometry (CTG), the size of trabeculae increases isometrically. These models produce fundamentally different patterns of surface area and volume scaling. We then compared the models with empirical observations of scaling of trabecular dimensions in mammals ranging in mass from 4 to 40x10(6)g. Trabecular size showed little dependence on body size, approaching one of our theoretical models (CTS). This result suggests that some elements of trabecular architecture may be driven by the requirements of maintaining adequate surface area for calcium homeostasis. Additionally, we found two key consequences of this strongly negative allometry. First, the connectivity among trabecular elements is qualitatively different for small versus large animals; trabeculae connect primarily to cortical bone in very small animals and primarily to other trabeculae in larger animals. Second, small animals have very few trabeculae and, as a consequence, we were able to identify particular elements with a consistent position across individuals and, for some elements, across species. Finally, in order to infer the possible influence of gross differences in mechanical loading on trabecular size, we sampled trabecular dimensions extensively within Chiroptera and compared their trabecular dimensions with those of non-volant mammals. We found no systematic differences in trabecular size or scaling patterns related to locomotor mode.