A systems identification approach using Bayes factors to deconstruct the brain bases of emotion regulation.

Cognitive reappraisal is fundamental to cognitive therapies and everyday emotion regulation. Analyses using Bayes factors and an axiomatic systems identification approach identified four reappraisal-related components encompassing distributed neural activity patterns across two independent functional magnetic resonance imaging (fMRI) studies (n = 182 and n = 176): (1) an anterior prefrontal system selectively involved in cognitive reappraisal; (2) a fronto-parietal-insular system engaged by both reappraisal and emotion generation, demonstrating a general role in appraisal; (3) a largely subcortical system activated during negative emotion generation but unaffected by reappraisal, including amygdala, hypothalamus and periaqueductal gray; and (4) a posterior cortical system of negative emotion-related regions downregulated by reappraisal. These systems covaried with individual differences in reappraisal success and were differentially related to neurotransmitter binding maps, implicating cannabinoid and serotonin systems in reappraisal. These findings challenge 'limbic'-centric models of reappraisal and provide new systems-level targets for assessing and enhancing emotion regulation.

CAR NK92 Cells Targeting BCMA Can Effectively Kill Multiple Myeloma Cells Both In Vitro and In Vivo.

Multiple myeloma (MM) is a hematological malignancy caused by malignant proliferation of plasma cells in bone marrow. Over the last decade, the survival outcome of patients with multiple myeloma (MM) has been substantially improved with the emergence of novel therapeutic agents. However, MM remains an incurable neoplastic plasma cell disorder. In addition, almost all MM patients inevitably relapse due to drug resistance. Chimeric antigen receptor (CAR)-modified NK cells represent a promising immunotherapeutic modality for cancer treatment. In this study, NK92 cells were engineered to express the third generation of BCMA CAR. In vitro, BCMA CAR-engineered NK92 cells displayed higher cytotoxicity and produced more cytokines such as IFN-γ and granzyme B than NK92 cells when they were co-cultured with MM cell lines. Furthermore, BCMA CAR-engineered NK92 cells released significantly higher amounts of cytokines and showed higher cytotoxicity when they were exposed to primary cells isolated from MM patients. The cytotoxicity of BCMA CAR NK92 cells was enhanced after MM cells were treated with bortezomib. Additionally, BCMA CAR NK92 cells exhibited potent antitumor activities in subcutaneous tumor models of MM. These results demonstrate that regional administration of BCMA CAR NK92 cells is a potentially promising strategy for treating MM.

Multilayer Coating with Red Ginseng Dietary Fiber Improves Intestinal Adhesion and Proliferation of Probiotics in Human Intestinal Epithelial Models.

To exert their beneficial effects, it is essential for the commensal bacteria of probiotic supplements to be sufficiently protected as they pass through the low pH environment of the stomach, and effectively colonize the intestinal epithelium downstream. Here, we investigated the effect of a multilayer coating containing red ginseng dietary fiber, on the acid tolerance, and the adhesion and proliferation capacities of three Lactobacillus strains (Limosilactobacillus reuteri KGC1901, Lacticaseibacillus casei KGC1201, Limosilactobacillus fermentum KGC1601) isolated from Panax ginseng, using HT-29 cells, mucin-coated plates, and human pluripotent stem cell-derived intestinal epithelial cells as in vitro models of human gut physiology. We observed that the multilayer-coated strains displayed improved survival rates after passage through gastric juice, as well as high adhesion and proliferation capacities within the various gut epithelial systems tested, compared to their uncoated counterparts. Our findings demonstrated that the multilayer coat effectively protected commensal microbiota and led to improved adhesion and colonization of intestinal epithelial cells, and consequently to higher probiotic efficacy.

Probiotic Characteristics and Safety Assessment of Lacticaseibacillus casei KGC1201 Isolated from Panax ginseng.

Panax ginseng is one of the most important herbal medicinal plants consumed as health functional food and can be fermented to achieve better efficacy. Lacticaseibacillus, one of the representative genera among lactic acid bacteria (LAB), has also been used as a probiotic material for health functional foods due to its beneficial effects on the human body. To achieve a synergistic effect by using these excellent dietary supplement ingredients together, a novel LAB strain was isolated from the root of 6-year-old ginseng. Through similarity analysis of 16S rRNAs and whole-genome sequences, the strain was confirmed as belonging to the genus Lacticaseibacillus and was named L. casei KGC1201. KGC1201 not only met all safety standards as food, but also showed excellent probiotic properties such as acid resistance, bile salt resistance, and intestinal adhesion. In particular, KGC1201 exhibited superior acid resistance through morphological observation identifying that the cell surface damage of KGC1201 was less than that of the L. casei type strain KCTC3109. Gene expression studies were conducted to elucidate the molecular mechanisms of KGC1201's acid resistance, and the expression of the glycosyltransferase gene was found to be significantly elevated under acidic conditions. Exopolysaccharides (EPSs) biosynthesized by glycosyltransferase were also increased in KGC1201 compared to KCTC3109, which may contribute to better protection of KGC1201 cells from strong acidity. Therefore, KGC1201, with its increased acid resistance through molecular mechanisms and excellent probiotic properties, can be used in health functional foods to provide greater benefit to overall human health and well-being.

Exopolysaccharide of Enterococcus faecium L15 promotes the osteogenic differentiation of human dental pulp stem cells via p38 MAPK pathway.

BACKGROUND: Bone has important functions in the body. Several researchers have reported that the polysaccharides and lipopolysaccharide derived from microbes can promote osteogenic differentiation of stem cells. Enterococcus faecium, a lactic acid bacterium (LAB), produces several bioactive metabolites and has been widely applied in the food and nutraceutical industries. The exopolysaccharide (EPS) from LAB has also been extensively examined for its postbiotic effects and for its in vivo and in vitro functionalities. However, studies on promoting bone differentiation using polysaccharides from LAB are lacking. Therefore, the purpose of this study was to investigate the effect of E. faecium L15 extract and EPS on osteogenic differentiation of human dental pulp stem cells (hDPSCs) and to identify the underlying mechanisms. METHODS: hDPSCs were obtained from dental pulp tissue, and L15 extract and EPS were isolated from L15. Gene and protein expression of the osteogenic differentiation markers were analyzed with qPCR and western blotting and the possible signaling pathways were also investigated using western blotting. Osteogenic differentiation potential was examined by alkaline phosphatase (ALP) staining and alizarin red s (ARS) staining. In addition, osteogenic differentiation potential of L15 EPS was explored in ex vivo culture of neonate murine calvaria. RESULTS: The calcium deposition and ALP activity were enhanced by addition of L15 extract or EPS. The expression levels of RUNX2, ALP, and COL1A1 mRNA and the protein expression levels of RUNX2, ALP, and BMP4 were increased in hDPSCs treated with the L15 extract or EPS. The L15 EPS treatment enhanced phosphorylation of the p38 mitogen-activated protein kinase (MAPK). The L15 EPS-induced increases in RUNX2, ALP, and BMP4 expression were suppressed by the p38 MAPK inhibitor SB203580. The promoting effect of L15 EPS on osteogenic differentiation was not only seen in hDPSCs, but also in osteoblast precursors. ALP activity and the expression of RUNX2, ALP, and COL1A1 increased in the L15 EPS-treated osteoblast precursors. In addition, L15 EPS increased bone thickness of neonate murine calvaria in ex vivo culture. CONCLUSIONS: The stimulatory effect of L15 extract and EPS on osteogenic differentiation occurred through the p38 MAPK pathway, and L15 EPS enhanced new bone formation in neonate murine calvaria. These data suggest that L15 EPS has therapeutic potential applicable to bone regeneration.

The Influence of Tyrosol-Enriched Rhodiola sachalinensis Extracts Bioconverted by the Mycelium of Bovista plumbe on Scopolamine-Induced Cognitive, Behavioral, and Physiological Responses in Mice.

Alzheimer's disease (AD) is an age-related neurodegenerative disorder characterized by cognitive deficits, which are accompanied by memory loss and cognitive disruption. Rhodiola sachalinensis (RSE) is a medicinal plant that has been used in northeastern Asia for various pharmacological activities. We attempted to carry out the bioconversion of RSE (Bio-RSE) using the mycelium of Bovista plumbe to obtain tyrosol-enriched Bio-RSE. The objective of this study was to investigate the effects of Bio-RSE on the activation of the cholinergic system and the inhibition of oxidative stress in mice with scopolamine (Sco)-induced memory impairment. Sco (1 mg/kg body weight, i.p.) impaired the mice's performance on the Y-maze test, passive avoidance test, and water maze test. However, the number of abnormal behaviors was reduced in the groups supplemented with Bio-RSE. Bio-RSE treatment improved working memory and avoidance times against electronic shock, increased step-through latency, and reduced the time to reach the escape zone in the water maze test. Bio-RSE dramatically improved the cholinergic system by decreasing acetylcholinesterase activity and regulated oxidative stress by increasing antioxidant enzymes (superoxide dismutase (SOD) and catalase (CAT)). The reduction in nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) signaling in the brain tissue due to scopolamine was restored by the administration of Bio-RSE. Bio-RSE also significantly decreased amyloid-beta 1-42 (Aß1-42) and amyloid precursor protein (APP) expression. Moreover, the increased malondialdehyde (MDA) level and low total antioxidant capacity in Sco-treated mouse brains were reversed by Bio-RSE, and an increase in Nrf2 and HO-1 was also observed. In conclusion, Bio-RSE protected against Sco-induced cognitive impairment by activating Nrf2/HO-1 signaling and may be developed as a potential beneficial material for AD.

Anti-Inflammatory Effects of Limosilactobacillus fermentum KGC1601 Isolated from Panax ginseng and Its Probiotic Characteristics.

We investigated the potential probiotic properties of Limosilactobacillus fermentum KGC1601 isolated from Panax ginseng. Ginseng cultivated in an experimental field of the Korea Ginseng Research Institute was fermented, followed by single colony selection from MRS agar. We performed 16s-rRNA sequencing and whole-genome analysis to identify L. fermentum and evaluate the biosafety parameters of this strain, respectively. We confirmed this strain was susceptible to six antibiotics, as proposed by the European Food Safety Authority, did not produce biogenic amines, and did not exhibit any hemolytic activity. Acid resistance and bile salt tolerance, which are essential properties of a probiotic agent, were investigated. Notably, distinguishing properties of this strain were that it exhibited excellent bile salt tolerance and anti-inflammatory effects. The excellent bile salt tolerance was confirmed by scanning electron microscopy. Through qRT-PCR and ELISA studies, it was revealed that L. fermentum KGC1601 pre-treatment up-regulates anti-inflammatory cytokines and down-regulates pro-inflammatory cytokines in RAW 264.7 cells. Consequently, we suggested that L. fermentum KGC1601 can be safely used as a potential anti-inflammatory functional probiotic agent.

Comparison of Cell-Free Extracts from Three Newly Identified Lactobacillus plantarum Strains on the Inhibitory Effect of Adipogenic Differentiation and Insulin Resistance in 3T3-L1 Adipocytes.

Obesity and associated metabolic disorders, including cardiovascular disease and diabetes, are rapidly becoming serious global health problems. It has been reported that Lactobacillus plantarum (L. plantarum) extracts have the beneficial activities of antiobesity and antidiabetes, although few studies have compared the beneficial effects among various L. plantarum extracts. In this study, three new L. plantarum (named LP, LS, and L14) strains were identified, and the antiobesogenic and diabetic effects of their extracts were investigated and compared using 3T3-L1 cells in vitro. Lipid accumulation in maturing 3T3-L1 cells was significantly decreased by the addition of LS and L14 extracts. The mRNA expression levels of Pparγ, C/ebpα, Fabp4, Fas, and Dgat1 were significantly decreased by the addition of LP, LS, and L14 extracts. Interestingly, the protein expression levels of PPARγ, C/EBPα, FABP4, and FAS were downregulated in mature 3T3-L1 cells with the addition of the L14 extract. Moreover, the LS and L14 extract treatments stimulated glucose uptake in maturing adipocytes. The L14 extract treatments exhibited a significant reduction in TNF-α protein expression, which is a key factor of insulin resistance in adipocytes. Of the three extracts, L14 extract markedly reduced adipogenic differentiation and insulin resistance in vitro, suggesting that the L14 extract may be used as a therapeutic agent for obesity-associated metabolic disorders.

Oral intake of Lactobacillus plantarum L-14 extract alleviates TLR2- and AMPK-mediated obesity-associated disorders in high-fat-diet-induced obese C57BL/6J mice.

OBJECTIVES: Whether periodic oral intake of postbiotics positively affects weight regulation and prevents obesity-associated diseases in vivo is unclear. This study evaluated the action mechanism of Lactobacillus plantarum L-14 (KTCT13497BP) extract and the effects of its periodic oral intake in a high-fat-diet (HFD) mouse model. MATERIALS AND METHODS: Mouse pre-adipocyte 3T3-L1 cells and human bone marrow mesenchymal stem cells (hBM-MSC) were treated with L-14 extract every 2 days during adipogenic differentiation, and the mechanism underlying anti-adipogenic effects was analysed at cellular and molecular levels. L-14 extract was orally administrated to HFD-feeding C57BL/6J mice every 2 days for 7 weeks. White adipose tissue was collected and weighed, and liver and blood serum were analysed. The anti-adipogenic mechanism of exopolysaccharide (EPS) isolated from L-14 extract was also analysed using Toll-like receptor 2 (TLR2) inhibitor C29. RESULTS: L-14 extract inhibited 3T3-L1 and hBM-MSC differentiation into mature adipocytes by upregulating AMPK signalling pathway in the early stage of adipogenic differentiation. The weight of the HFD + L-14 group (31.51 ± 1.96 g) was significantly different from that of the HFD group (35.14 ± 3.18 g). L-14 extract also significantly decreased the serum triacylglycerol/high-density lipoprotein cholesterol ratio (an insulin resistance marker) and steatohepatitis. In addition, EPS activated the AMPK signalling pathway by interacting with TLR2, consequently inhibiting adipogenesis. CONCLUSIONS: EPS from L-14 extract inhibits adipogenesis via TLR2 and AMPK signalling pathways, and oral intake of L-14 extract improves obesity and obesity-associated diseases in vivo. Therefore, EPS can be used to prevent and treat obesity and metabolic disorders.

Exopolysaccharide Isolated from Lactobacillus plantarum L-14 Has Anti-Inflammatory Effects via the Toll-Like Receptor 4 Pathway in LPS-Induced RAW 264.7 Cells.

Inflammation is a biological response of the immune system to defend the body from negative stimulation. However, the excessive inflammatory response can damage host tissues and pose serious threats. Exopolysaccharide (EPS), one of the postbiotics, is secreted from lactic acid bacteria. Although many studies have described the beneficial effects of EPS, such as its anti-inflammatory and anti-oxidant effects, its underlying mechanisms have remained to be poorly understood. Thus, we identified that EPS obtained from Lactobacillus plantarum L-14 was a homogeneous polysaccharide primarily comprised of glucose. To examine these anti-inflammatory effects, an inflammatory response was induced by lipopolysaccharide (LPS) administration to mouse macrophage RAW 264.7 cells that were pretreated with EPS. The anti-inflammatory effects of EPS were identified by analyzing the changes within inflammatory markers at the molecular level. We demonstrate here that EPS suppressed proinflammatory mediators, such as cyclooxygenase-2, interleukin-6, tumor necrosis factor-α, and interleukin-1ß, and downregulated the expression of an inducible nitric oxide synthase known to lead to oxidative stress. It was also confirmed that EPS had anti-inflammatory effects by blocking the interaction of LPS with Toll-like receptor 4 (TLR4), as demonstrated by using the known TLR4 inhibitor TAK-242. In addition, we found that EPS itself could suppress the expression of TLR4. Consequently, our data suggest that EPS can be a potential target for the development of natural product-derived medicine for treating inflammatory diseases related to TLR4.

The Multiple Ingredients Effect: The More Diverse (Un)Healthy Ingredients, the More (Un)Healthy the Food.

BACKGROUND: Although previous research has demonstrated that ingredient information plays a significant role in consumers' healthier food choices, none of the research has investigated how the number of ingredients (ie, single vs multiple) influences consumer perceptions of food healthiness. However, this research argues that consumers have lay belief that the greater the number of (un)healthy ingredients in food, the more (un)healthy the food is perceived and they rely on the lay belief when judging food healthiness. Thus, this paper proposes and examines the multiple ingredients effect that people make inferences about food (un)healthiness based on the diversity of (un)healthy ingredients. METHODS AND RESULTS: Four studies test our hypotheses using ANOVAs and regression analyses. Study 1 examines that people indicate a higher perception of food unhealthiness when the number of unhealthy ingredients is presented as multiple rather than single. Study 2 replicates the multiple ingredients effect in the healthy food domain and eliminates an alternative explanation based on the subadditivity effect. Study 3 also finds that the difference in food healthiness perception between people who have high and low health consciousness is driven by the salience of each ingredient. Finally, Study 4 identifies the evaluability of the nutritional value as a boundary condition for our effect in an AI-based self-service context. CONCLUSION: The current research demonstrates the multiple ingredients effect that people perceive higher food (un)healthiness when the number of (un)healthy ingredients is greater although nutritional information is identically presented. Moreover, this effect is moderated by the extent to which people are conscious of health-related issues. This finding is because ingredient information is highly accessible and salient for health-conscious people .

Anti-Cancer Effects of Lactobacillus plantarum L-14 Cell-Free Extract on Human Malignant Melanoma A375 Cells.

Human malignant melanoma is the most aggressive type of skin cancer with high metastatic ability. Despite several traditional therapies, the mortality rate remains high. Lactobacillus plantarum (L. plantarum), a species of lactic acid bacteria (LAB), is being studied for human health, including cancer treatment. However, few studies have elucidated the relationship between L. plantarum extract and human malignant melanoma. To investigate the effects of L. plantarum on human melanoma cells, A375 human melanoma cells were used and treated with L. plantarum L-14 extract. After the treatment, viability, migration ability, molecular changes of migration- and apoptosis-related genes, and the location of cytochrome c was evaluated. The L-14 extract inhibited the viability, migration of A375 cells as well as reduced expression of migration-related genes. In addition, it was confirmed that the L-14 extract induced intrinsic apoptosis in A375 cells. This study demonstrated that the L-14 extract exerted anticancer effects on A375 cells. Therefore, these data suggest that the L-14 extract is worth studying for the development of melanoma drugs using LAB.

Cell-Penetrating Peptides Enhance the Activity of Human Fibroblast Growth Factor 2 by Prolonging the Retention Time: A New Vision for Drug-Delivery Systems.

Cell-penetrating peptides (CPPs) are defined by their ability to deliver cargo into cells and have been studied and developed as a promising drug-delivery system (DDS). However, the issue of whether the CPPs that have already entered the cells can be re-released or reused has not been studied. The purpose of this research was to construct CPP-conjugated human fibroblast growth factor 2 (hFGF2) and investigate whether they can be re-released from the cell membrane for reuse. This study combined hFGF2 with Tat or Ara27, a newly developed CPP derived from the zinc knuckle (CCHC-type) family protein of Arabidopsis. Human dermal fibroblast (HDF) was treated with Tat-conjugated hFGF2 (tFGF2) and Ara27-conjugated hFGF2 (NR-FGF2) for both long and short durations, and the effects on cell growth were compared. Furthermore, tFGF2 and NR-FGF2 re-released from the cells were quantified and the effects were evaluated by culturing HDF in a conditioned medium. Interestingly, the proliferation of HDF increased only when NR-FGF2 was treated for 1 h in endocytosis-independent manner. After 1 h, NR-FGF2 was significantly re-released, reaching a maximum concentration at 5 h. Furthermore, increased proliferation of HDF cultured in the conditioned medium containing re-released NR-FGF2 was discovered. While previous studies have focused on the delivery of cargo and its associated applications, this study has revealed that combinations of superior CPPs and therapeutics can be expected to prolong both the retention time and the cell-penetrating capacity, even in the presence of external factors. Therefore, CPPs can be applied in the context of topical drugs and cosmetics as a new DDS approach.

Gamma Irradiated Rhodiola sachalinensis Extract Ameliorates Testosterone-Induced Benign Prostatic Hyperplasia by Downregulating 5-Alpha Reductase and Restoring Testosterone in Rats.

The effect of Rhodiola sachalinensis Boriss extract irradiated with 50 kGy gamma rays (HKC) on benign prostatic hyperplasia (BPH) was investigated. Seven-week-old male SD rats received a subcutaneous injection of 20 mg/kg of testosterone propionate (TP) to induce BPH. Then, the testosterone only group received testosterone, the testosterone + finasteride group received testosterone and finasteride (5 mg/kg), the testosterone + HKC group received testosterone and HKC extract (500 mg/kg). Prostate weight and the dihydrotestosterone (DHT) levels in serum or prostate tissue were determined. The mRNA expressions of 5-alpha reductase (AR) in prostate tissue were also measured. Compared to the control group, prostate weight was significantly improved in the TP group and decreased in the HKC and finasteride-treated groups. Furthermore, the mRNA expression of 5-AR in the prostate was significantly reduced in the HKC and finasteride-treated groups. Similarly, the expression levels of α-smooth muscle actin (α-SMA) and cytokeratin, which are associated with prostatic enlargement in the HKC and finasteride groups, were much lower than in the TP group. HKC treatment showed similar efficacy to finasteride treatment on rats with testosterone-induced BPH. HKC may be explored as a potential new drug for BPH treatment.

CODA-ML: context-specific biological knowledge representation for systemic physiology analysis.

BACKGROUND: Computational analysis of complex diseases involving multiple organs requires the integration of multiple different models into a unified model. Different models are often constructed in heterogeneous formats. Thus, the integration of the models requires a standard language format that can effectively represent essential biological information. However, the previously introduced formats have limitations that prevent from adequately representing essential biological information, particularly specifications of bio-molecules and biological contexts. RESULTS: We defined an XML-based markup language called context-oriented directed association markup language (CODA-ML), which better represents essential biological information. The CODA-ML has two major strengths in designating molecular specifications and biological contexts. It can cover heterogeneous entity types involved in biological events (e.g. gene/protein, compound, cellular function, disease). Molecular types of entities can have molecular specifications which include detailed information of a molecule from isoforms to modifications, enabling high-resolution representation of molecules. In addition, it can distinguish biological events that vary depending on different biological contexts such as cell types or disease conditions. Especially representation of inter-cellular events as well as intra-cellular events is available. These two major strengths can resolve contradictory associations when different models are integrated into one unified model, which improves the accuracy of the model. CONCLUSIONS: With the CODA-ML, diverse models such as signaling pathways, metabolic pathways, and gene regulatory pathways can be represented in a unified language format. Heterogeneous entity types can be covered by the CODA-ML, thus it enables detailed description for the mechanisms of diseases or drugs from multiple perspectives (e.g., molecule, function or disease). The CODA-ML is expected to help integrate different models into one systemic model in an efficient and effective. The unified model can be used to perform computational analysis not only for cancer but also for other complex diseases involving multiple organs beyond a single cell.

Deconvoluting essential gene signatures for cancer growth from genomic expression in compound-treated cells.

MOTIVATION: Essential gene signatures for cancer growth have been typically identified via RNAi or CRISPR-Cas9. Here, we propose an alternative method that reveals the essential gene signatures by analysing genomic expression profiles in compound-treated cells. With a large amount of the existing compound-induced data, essential gene signatures at genomic scale are efficiently characterized without technical challenges in the previous techniques. RESULTS: An essential gene is characterized as a gene presenting positive correlation between its down-regulation and cell growth inhibition induced by diverse compounds, which were collected from LINCS and CGP. Among 12 741 genes, 1092, 1 228 827 962, 1 664 580 and 829 essential genes are characterized for each of A375, A549, BT20, LNCAP, MCF7, MDAMB231 and PC3 cell lines (P-value ≤ 1.0E-05). Comparisons to the previously identified essential genes yield significant overlaps in A375 and A549 (P-value ≤ 5.0E-05) and the 103 common essential genes are enriched in crucial processes for cancer growth. In most comparisons in A375, MCF7, BT20 and A549, the characterized essential genes yield more essential characteristics than those of the previous techniques, i.e. high gene expression, high degrees of protein-protein interactions, many homologs and few paralogs. Remarkably, the essential genes commonly characterized by both the previous and proposed techniques show more significant essential characteristics than those solely relied on the previous techniques. We expect that this work provides new aspects in essential gene signatures. AVAILABILITY AND IMPLEMENTATION: The Python implementations are available at https://github.com/jmjung83/deconvolution_of_essential_gene_signitures. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publisher Correction: CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy.

BACKGROUND: Muscle atrophy, an involuntary loss of muscle mass, is involved in various diseases and sometimes leads to mortality. However, therapeutics for muscle atrophy thus far have had limited effects. Here, we present a new approach for therapeutic target prediction using Petri net simulation of the status of phosphorylation, with a reasonable assumption that the recovery of abnormally phosphorylated proteins can be a treatment for muscle atrophy. RESULTS: The Petri net model was employed to simulate phosphorylation status in three states, i.e. reference, atrophic and each gene-inhibited state based on the myocyte-specific phosphorylation network. Here, we newly devised a phosphorylation specific Petri net that involves two types of transitions (phosphorylation or de-phosphorylation) and two types of places (activation with or without phosphorylation). Before predicting therapeutic targets, the simulation results in reference and atrophic states were validated by Western blotting experiments detecting five marker proteins, i.e. RELA, SMAD2, SMAD3, FOXO1 and FOXO3. Finally, we determined 37 potential therapeutic targets whose inhibition recovers the phosphorylation status from an atrophic state as indicated by the five validated marker proteins. In the evaluation, we confirmed that the 37 potential targets were enriched for muscle atrophy-related terms such as actin and muscle contraction processes, and they were also significantly overlapping with the genes associated with muscle atrophy reported in the Comparative Toxicogenomics Database (p-value < 0.05). Furthermore, we noticed that they included several proteins that could not be characterized by the shortest path analysis. The three potential targets, i.e. BMPR1B, ROCK, and LEPR, were manually validated with the literature. CONCLUSIONS: In this study, we suggest a new approach to predict potential therapeutic targets of muscle atrophy with an analysis of phosphorylation status simulated by Petri net. We generated a list of the potential therapeutic targets whose inhibition recovers abnormally phosphorylated proteins in an atrophic state. They were evaluated by various approaches, such as Western blotting, GO terms, literature, known muscle atrophy-related genes and shortest path analysis. We expect the new proposed strategy to provide an understanding of phosphorylation status in muscle atrophy and to provide assistance towards identifying new therapies.

Author Correction: CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects.

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.

Protein extracted from Porphyra yezoensis prevents cisplatin-induced nephrotoxicity by downregulating the MAPK and NF-κB pathways.

Acute renal failure is a serious complication of treatment with the anticancer drug cisplatin. Cisplatin exerts a cytotoxic effect on renal cells by inducing apoptosis through activating the tumor suppressor p53, nuclear factor­κB (NF­κB) and mitogen­activated protein kinase (MAPK)/p38 pathways. Effects of protein extracts of the brown seaweed Porphyra yezoensis (P. yezoensis) on cytotoxicity, inflammation and cell proliferation have been reported; however, the effects of P. yezoensis protein (PYP) extract on cisplatin­induced renal injury have remained elusive. The present study investigated the effects of PYP on cisplatin­induced nephrotoxicity in the HK2 human proximal tubular epithelial cell line. PYP treatment reduced cisplatin­induced apoptosis and death of HK2 cells by restoring the B­cell lymphoma­2 (Bcl­2)­associated X protein (Bax)/Bcl­2 imbalance, cytochrome c release and caspase­3 activation. In addition, PYP activated the redox­sensitive transcription factor NF­κB via stimulating the nuclear translocation of p65 in HK2 cells. PYP also restored renal antioxidant levels and increased the total and nuclear accumulation of NF erythroid 2­related factor 2 in HK2 cells. PYP markedly attenuated cisplatin­induced p38, MAPK and c­Jun N­terminal kinase phosphorylation. Furthermore, treatment with PYP ameliorated cisplatin­induced renal cell damage by upregulating antioxidant defense mechanisms and downregulating the MAPK and NF­κB signaling pathways. In addition, mice were divided into three treatment groups (control, cisplatin and PYP + cisplatin) and the effects of PYP were evaluated in a mouse model of cisplatin­induced acute kidney injury. The concentrations of blood urea nitrogen and serum creatinine in the PYP + cisplatin group were lower than those in the cisplatin group. The mRNA expression levels of inflammatory factors interleukin­6 (IL­6), IL­1ß, tumor necrosis factor­α and monocyte chemoattractant protein­1 in the kidney tissues of the PYP + cisplatin group were also lower than those in the cisplatin group. These results suggest that PYP treatment had a preventive effect on nephrotoxicity, specifically by downregulating the MAPK and NF­κB signaling pathways and the mRNA levels of inflammatory genes.