Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations.

Natural products have successfully treated several diseases using a multi-component, multi-target mechanism. However, a precise mechanism of action (MOA) has not been identified. Systems pharmacology methods have been used to overcome these challenges. However, there is a limitation as those similar mechanisms of similar components cannot be identified. In this study, comparisons of physicochemical descriptors, molecular docking analysis and RNA-seq analysis were performed to compare the MOA of similar compounds and to confirm the changes observed when similar compounds were mixed and used. Various analyses have confirmed that compounds with similar structures share similar MOA. We propose an advanced method for in silico experiments in herbal medicine research based on the results. Our study has three novel findings. First, an advanced network pharmacology research method was suggested by partially presenting a solution to the difficulty in identifying multi-component mechanisms. Second, a new natural product analysis method was proposed using large-scale molecular docking analysis. Finally, various biological data and analysis methods were used, such as in silico system pharmacology, docking analysis and drug response RNA-seq. The results of this study are meaningful in that they suggest an analysis strategy that can improve existing systems pharmacology research analysis methods by showing that natural product-derived compounds with the same scaffold have the same mechanism.

Gene expression profiling of nasal inflammation induced by diesel particles using an in vivo system.

Korean diesel particulate matter 20 (KDP20) is a pollutant comprising a complex mixture of carbon and chemical irritants. Although particulate matter and nasal inflammation are strongly associated, the underlying molecular mechanism based on systematic transcriptome analysis remains unknown. In this study, genome-wide gene expression profiles of mouse nasal tissues were determined following exposure to KDP20 for 5 and 10 days and compared with those of the control (n = 4/group). We identified 758 significant differentially expressed genes (DEGs) and classified them as 5-day-specific, 10-day-specific, and common among groups based on their expression patterns. The terms "regulation of alpha-beta T cell differentiation," "macrophage differentiation," and "cell adhesion mediated by integrin" were significantly enriched in each group. Receiver operating characteristic analysis revealed six genes as potential predictive biomarkers. The differential expression of these six genes was validated using quantitative RT-PCR (n = 3/group). Furthermore, a possible mechanism for nasal inflammation was suggested through the binding analysis between metal ions and genes. The genes identified in this study may play important roles in regulating the mechanism of nasal inflammation induced by diesel particles, especially immune cell regulation, and may function as markers for diesel particle-induced nasal inflammation.

miR-431 promotes differentiation and regeneration of old skeletal muscle by targeting Smad4.

The myogenic capacity of myoblasts decreases in skeletal muscle with age. In addition to environmental factors, intrinsic factors are important for maintaining the regenerative potential of muscle progenitor cells, but their identities are largely unknown. Here, comparative analysis of microRNA (miRNA) expression profiles in young and old myoblasts uncovered miR-431 as a novel miRNA showing markedly reduced abundance in aged myoblasts. Importantly, elevating miR-431 improved the myogenic capacity of old myoblasts, while inhibiting endogenous miR-431 lowered myogenesis. Bioinformatic and biochemical analyses revealed that miR-431 directly interacted with the 3' untranslated region (UTR) of Smad4 mRNA, which encodes one of the downstream effectors of TGF-ß signaling. In keeping with the low levels of miR-431 in old myoblasts, SMAD4 levels increased in this myoblast population. Interestingly, in an in vivo model of muscle regeneration following cardiotoxin injury, ectopic miR-431 injection greatly improved muscle regeneration and reduced SMAD4 levels. Consistent with the finding that the mouse miR-431 seed sequence in the Smad4 3' UTR is conserved in the human SMAD4 3' UTR, inhibition of miR-431 also repressed the myogenic capacity of human skeletal myoblasts. Taken together, our results suggest that the age-associated miR-431 plays a key role in maintaining the myogenic ability of skeletal muscle with age.

Identification of Epigenetic Mechanisms Involved in the Anti-Asthmatic Effects of Descurainia sophia Seed Extract Based on a Multi-Omics Approach.

Asthma, a heterogeneous disease of the airways, is common around the world, but little is known about the molecular mechanisms underlying the interactions between DNA methylation and gene expression in relation to this disease. The seeds of Descurainia sophia are traditionally used to treat coughs, asthma and edema, but their effects on asthma have not been investigated by multi-omics analysis. We undertook this study to assess the epigenetic effects of ethanol extract of D. sophia seeds (DSE) in an ovalbumin (OVA)-induced mouse model of asthma. We profiled genome-wide DNA methylation by Methyl-seq and characterized the transcriptome by RNA-seq in mouse lung tissue under three conditions: saline control, OVA-induced, and DSE-treated. In total, 1995 differentially methylated regions (DMRs) were identified in association with anti-asthmatic effects, most in promoter and coding regions. Among them, 25 DMRs were negatively correlated with the expression of the corresponding 18 genes. These genes were related to development of the lung, respiratory tube and respiratory system. Our findings provide insights into the anti-asthmatic effects of D. sophia seeds and reveal the epigenetic targets of anti-inflammatory processes in mice.

SERBP1 affects homologous recombination-mediated DNA repair by regulation of CtIP translation during S phase.

DNA double-strand breaks (DSBs) are the most severe type of DNA damage and are primarily repaired by non-homologous end joining (NHEJ) and homologous recombination (HR) in the G1 and S/G2 phase, respectively. Although CtBP-interacting protein (CtIP) is crucial in DNA end resection during HR following DSBs, little is known about how CtIP levels increase in an S phase-specific manner. Here, we show that Serpine mRNA binding protein 1 (SERBP1) regulates CtIP expression at the translational level in S phase. In response to camptothecin-mediated DNA DSBs, CHK1 and RPA2 phosphorylation, which are hallmarks of HR activation, was abrogated in SERBP1-depleted cells. We identified CtIP mRNA as a binding target of SERBP1 using RNA immunoprecipitation-coupled RNA sequencing, and confirmed SERBP1 binding to CtIP mRNA in S phase. SERBP1 depletion resulted in reduction of polysome-associated CtIP mRNA and concomitant loss of CtIP expression in S phase. These effects were reversed by reconstituting cells with wild-type SERBP1, but not by SERBP1 ΔRGG, an RNA binding defective mutant, suggesting regulation of CtIP translation by SERBP1 association with CtIP mRNA. These results indicate that SERBP1 affects HR-mediated DNA repair in response to DNA DSBs by regulation of CtIP translation in S phase.

Aberrant upregulation of ASCL2 by promoter demethylation promotes the growth and resistance to 5-fluorouracil of gastric cancer cells.

Achaete scute-like 2 (ASCL2), a basic helix-loop-helix transcription factor, plays an essential role in the maintenance of adult intestinal stem cells. However, the function of ASCL2 in gastric cancer (GC) is poorly understood. Therefore, we investigated the roles and regulatory transcription mechanisms of ASCL2 in GC. Gene expression and methylation data analysis showed that ASCL2 was upregulated and hypomethylated in GC tissues. Using real-time RT-PCR and pyrosequencing analysis, we confirmed that ASCL2 was overexpressed and hypomethylated in GC tissues compared to adjacent normal tissues. We then investigated the mechanisms underlying the aberrant expression of ASCL2 in GC and found that treatment with a methylation inhibitor induced ASCL2 expression in GC cell lines. MBD-sequencing assay also revealed hypermethylation of the promoter region of ASCL2 in GC cell lines, which barely expressed the ASCL2 gene. Furthermore, ASCL2 expression levels were inversely correlated with GC patient survival. Ectopic overexpression of ASCL2 showed that ASCL2 increased cell growth and promoted resistance to 5-fluorouracil in GC cells. These results suggest that ASCL2 might play an important role in gastric tumor growth and chemoresistance, and could be a useful prognostic marker for GC patients.

Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes.

Background: Herbal medicines traditionally target organs for treatment based on medicinal properties, and this theory is widely used for prescriptions. However, the scientific evidence explaining how herbs act on specific organs by biological methods has been still limited. This study used bioinformatic tools to identify the target organ locations of Radix Achyranthis Bidentatae (RAB), a blood-activating herb that nourishes the liver and kidney, strengthens bones, and directs prescription to the lower body. Methods: RAB's active compounds and targets were collected and predicted using databases such as TCMSP, HIT2.0, and BATMAN-TCM. Next, the RAB's target list was analyzed based on two approaches to obtain target organ locations. DAVID and Gene ORGANizer enrichment-based approaches were used to enrich an entire gene list, and the BioGPS and HPA gene expression-based approaches were used to analyze the expression of core genes. Results: RAB's targets were found to be involved in whole blood, blood components, and lymphatic organs across all four tools. Each tool indicated a particular aspect of RAB's target organ locations: DAVID-enriched genes showed a predominance in blood, liver, and kidneys; Gene ORGANizer showed the effect on low body parts as well as bones and joints; BioGPS and HPA showed high gene expression in bone marrow, lymphoid tissue, and smooth muscle. Conclusion: Our bioinformatics-based target organ location prediction can serve as a modern interpretation tool for the target organ location theory of traditional medicine. Future studies should predict therapeutic target organ locations in complex prescriptions rather than single herbs and conduct experiments to verify predictions.

An Ethanol Extract of Coptidis rhizoma Induces Apoptotic Cell Death in Induced Pluripotent Stem Cells and Suppresses Teratoma Formation.

In cell-based regenerative medicine, induced pluripotent stem cells (iPSCs) generated from reprogrammed adult somatic cells have emerged as a useful cell source due to the lack of ethical concerns and the low risk of immune rejection. To address the risk of teratoma formation, which is a safety issue in iPSC-based cell therapy, it is essential to selectively remove undifferentiated iPSCs remaining in the iPSC-derived differentiated cell product prior to in vivo transplantation. In this study, we explored whether an ethanol extract of coptidis rhizoma (ECR) exhibited anti-teratoma activity and identified the active components involved in the selective elimination of undifferentiated iPSCs. Transcriptome analysis of iPSCs confirmed that cell death-related pathways were significantly altered by ECR treatment. Our results demonstrate that ECR effectively induced apoptotic cell death and DNA damage in iPSCs, and that reactive oxygen species generation, mitochondrial damage, caspase activation, and p53 activation were involved in ECR-mediated iPSC death. However, in iPSC-derived differentiated cells (iPSC-Diff), reduced cell viability and the DNA damage response were not observed after ECR treatment. We co-cultured iPSCs and iPSC-Diff and found that ECR treatment selectively removed iPSCs, whereas iPSC-Diff remained intact. Prior to in ovo implantation, ECR treatment of a mixed cell culture of iPSCs and iPSC-Diff significantly suppressed iPSC-derived teratoma formation. Among the main components of the ECR, berberine and coptisine showed selective cytotoxicity to iPSCs but not to iPSC-Diff. Together, these results indicate the usefulness of ECRs in preparing safe and effective iPSC-based therapeutic cell products with no risk of teratoma formation.

Supplementary data for genome-wide DNA methylation and gene expression analysis of PBMCs in patients with metabolic syndrome.

This supplementary data supports the research article 'Genome-wide DNA methylation profiling reveals candidate biomarkers and probable molecular mechanism of metabolic syndrome' (Baek et al., in press). To obtain these data, 32 participants with metabolic syndrome (MetS) were enrolled in the associated study. We collected peripheral blood mononuclear cells (PBMCs) from 11 patients with MetS and nine controls and compared genome-wide gene expression and DNA methylation signatures. The remaining 12 participants were used for the experimental validation of the candidate groups. We provide the raw, analyzed, and filtered genome-wide DNA methylation data, obtained using the Infinium Human MethylationEPIC BeadChIP array, and whole transcriptome sequencing data (accession number GSE181647). We list the differentially expressed and differentially methylated genes and their biological functions. These data can serve as a basis for screening appropriate epigenetic biomarkers for MetS.

Systematic Analysis of the Molecular Mechanisms of Cold and Hot Properties of Herbal Medicines.

Effective treatments for patients experiencing temperature-related symptoms are limited. The hot and cold effects of traditional herbal medicines have been utilized to treat and manage these symptoms, but their molecular mechanisms are not fully understood. Previous studies with arbitrarily selected herbs and ingredients may have produced biased results. Here, we aim to systematically elucidate the molecular mechanisms of the hot and cold properties of herbal medicines through an unbiased large-scale investigation of herbal ingredients, their target genes, and the transcriptome signatures induced by them. Using data regarding 243 herbs retrieved from two herbal medicine databases, we statistically identify (R)-Linalool, (-)-alpha-pinene, peruviol, (L)-alpha-terpineol, and cymol as five new hot-specific ingredients that share a common target, a norepinephrine transporter. However, no significant ingredients are cold-specific. We also statistically identify 14 hot- and 8 cold-specific new target genes. Pathway enrichment analysis of hot-specific target genes reveals the associated pathways including neurotransmitter reuptake, cold-induced thermogenesis, blood pressure regulation, adrenergic receptor signaling, and cation symporter activity. Cold-specific target genes are associated with the steroid pathway. Transcriptome analysis also shows that hot herbs are more strongly associated with coagulation and synaptic transmission than cold herbs. Our results, obtained from novel connections between herbal ingredients, target genes, and pathways, may contribute to the development of pharmacological treatment strategies for temperature-related pain using medicinal plants.

Identification of a novel anticancer mechanism of Paeoniae Radix extracts based on systematic transcriptome analysis.

Paeoniae Radix (PR) has a great therapeutic value in many clinical applications; however, the presence of various bioactive compounds and its complicated effects on human health makes its precise mechanisms of action unclear. This study investigated the effects of PR at the molecular pathway level by profiling genome-wide gene expression changes following dose-dependent treatment of human lung cancer cells (A549) with PR water extract (WPR), PR ethanol extracts (EPR), as well as their individual components. We found that PR exerts anticancer effects in A549 cells by regulating numerous pathways. Specifically, EPR and two compounds, namely, hederagenin (HG) and oleanolic acid (OA), significantly downregulate the Aurora B pathway. Furthermore, we generated an integrated PR extracts-compounds-target genes network in the Aurora B pathway to understand their interactions. Our findings reinforce that inhibiting Aurora kinase activity is a therapeutic target for treating cancers, providing the potential for novel mechanisms of action for PR and its components against lung cancer.

Systematic transcriptome analysis reveals molecular mechanisms and indications of bupleuri radix.

Pharmacogenomic analysis based on drug transcriptomic signatures is widely used to identify mechanisms of action and pharmacological indications. Despite accumulating reports on the efficacy of medicinal herbs, related transcriptome-level analyses are lacking. The aim of the present study was to elucidate the underlying molecular mechanisms of action of Bupleuri Radix (BR), a widely used herbal medicine, through a systematic transcriptomic analysis. We analyzed the drug-responsive transcriptome profiling of A549 lung cancer cell line after treating them with multiple doses of BR water (W-BR) and ethanol (E-BR) extracts and their phytochemicals. In vitro validation experiments were performed using both A549 and the immortalized human keratinocyte line HaCaT. Pathway enrichment analysis revealed the anti-cancer effects of BR treatment via inhibition of cell proliferation and induction of apoptosis. Enhanced cell adhesion and migration were observed with the W-BR but not with the E-BR. Comparison with a disease signature database validated an indication of the W-BR for skin disorders. Moreover, W-BR treatment showed the wound-healing effect in skin and lung cells. The main active ingredients of BR showed only the anti-cancer effect of the E-BR and not the wound healing effect of the W-BR, suggesting the need for research on minor ingredients of BR.

Circulating microRNAs as Potential Diagnostic Biomarkers for Poor Sleep Quality.

PURPOSE: Persistent poor sleep quality leads to impaired cognitive performance and an inability to perform daily activities. Biomarker-assisted diagnosis is important for the early treatment of poor sleep quality; however, diagnostic biomarkers for poor sleep quality remain unidentified. Circulating microRNAs (miRNAs) have been reported to be linked to the pathogenesis of poor sleep quality, indicating their possible role in sleep problem diagnosis. The present study aimed to identify potential miRNA biomarkers for poor sleep quality. PATIENTS AND METHODS: Differentially expressed serum miRNAs in patients with poor sleep quality and healthy controls (n=20) were analyzed via small RNA sequencing. Two-step quantitative RT-PCR in the two independent populations and receiver operating characteristic (ROC) analyses were used to validate the identified miRNAs. In silico analysis was then used to identify the target genes. RESULTS: Of the 59 circulating miRNAs identified via differential analysis, six were validated for differential expression by quantitative RT-PCR (n=60). Two of these six miRNAs, miR-4433b-3p and miR-619-5p, were reconfirmed in the second validation with an independent validation cohort (n=59). ROC analyses (n=40) revealed the probability of the two miRNAs as potential biomarkers with areas under the ROC curve (AUCs) of 0.81 and 0.70, respectively. The combined AUC was 0.86, which was much higher than that of each miRNA. Using in silico target gene analysis, the target genes of the two miRNAs were identified to be associated with the regulation of the circadian rhythm and inflammatory pathways. CONCLUSION: Our results revealed that miR-619-5p and miR-4433b-3p could be developed as potential diagnostic biomarkers for poor sleep quality. The combination of both miRNAs may be more effective than the use of the individual miRNA for sleep problem diagnosis.

Response to Transforaminal Epidural Block as a Useful Predictive Factor of Postherpetic Neuralgia.

Despite the high frequency of nerve blocks in the acute phase of herpes zoster, factors associated with intervention, such as response to epidural block, have not been analyzed as predictive factors of postherpetic neuralgia (PHN). To determine the predictive factors of progression to PHN in the presence of interventions, we analyzed the medical records of 145 patients who underwent transforaminal epidural injection (TFEI) in the acute phase of herpes zoster. A total volume of 5 mL (a mixture of 0.5% lidocaine and 5 mg dexamethasone) was injected during TFEI. Corticosteroid was used only for the first TFEI. Clinical data of age, sex, involved dermatome, presence of comorbidity, time from zoster onset to first TFEI, numerical rating scale (NRS) before TFEI, NRS at 1 week and 1, 3, and 6 months after the first TFEI, and number of TFEI were collected and analyzed. Through multivariate logistic regression analysis, pain improvement less than 50% at 1 week after the first TFEI was a strong predictive factor of progression of PHN at all time points. Response to TFEI appears to be a stronger predictive factor of progression to PHN than patient factors of sex, age, degree of initial pain, and presence of co-morbidity.

Effect of temperature on stacking orientations of zinc phthalocyanine thin films.

This paper reports the structural and optical properties of zinc phthalocyanine (ZnPc) thin films, prepared by thermal evaporation method, and their stacking dependence on the substrate temperature. The thickness of the films was measured by a quartz crystal monitor. X-ray diffraction analysis of the vacuum evaporated ZnPc films identified a phase transformation of metastable alpha-ZnPc phase to stable beta-ZnPc phase due to variation in the substrate temperature. The crystallite size (D), dislocation density (delta) and strain (epsilon) were calculated. The transmittance and absorbance spectra were recorded in the wavelength range 300-2500 nm using a UV-vis spectrophotometer. As the temperature was increased from room temperature to 200 degrees C, the band gap energy was decreased from 1.82 eV to 1.67 eV. The phase transformation was also confirmed by optical studies.

Enhanced performance of blue polymer light-emitting diodes by a self-assembled thin interlayer.

High efficiency and long lifetime, blue polymer light-emitting diodes were obtained by adding a thin interlayer, which was fabricated by a layer-by-layer self-assembly technique between poly(3,4-ethylene dioxythiophene)-poly(styrene sulfonic acid) (PEDOT:PSS) hole transporting and emissive polymer layers in the device configuration of indium tin oxide (ITO)/PEDOT:PSS (65 nm)/interlayer (10-30 nm)/emissive polymer (70 nm)/BaF2 (2 nm)/Ca (50 nm)/Al (300 nm). The interlayer, (PPV/PSS)n, consisted of self-assembled multilayers of the conjugated polymer, poly (p-phenylenevinylene) (PPV), and the polyelectrolyte, poly (styrene sulfonic acid) (PSS). Electroluminescence (EL) characteristics such as luminescence and current efficiency of the devices were enhanced by the addition of the interlayer. Furthermore, the devices with interlayer showed longer lifetime than those without interlayer. The maximum device performance was obtained from the device with (PPV/PSS)3 interlayer.

Heterojunction of hydrophobic poly(1,4-phenylenevinylene) and hydrophilic PEDOT:PSS on hydrophilic CdS nanoparticles.

Heterojunction of hydrophobic poly(1,4-phenylenevinylene) (PPV) on hydrophilic CdS nanoparticles was successfully prepared by the multi-layering of poly(p-xylene tetrahydrothiophenium chloride) (pre-PPV: precursor of PPV polymer) and poly(3,4-ethylenedioxythiophene)/poly(styrene sulfonate) (PEDOT:PSS) in an aqueous solution followed by a thermal treatment. CdS nanoparticles thin films were prepared on tin-doped indium oxide (ITO) by a chemical-bath-deposition method. The CdS surface was hydrophilic with low water contact angle of 15 degrees. Positively charged and water-soluble pre-PPV was used to form multilayers with PEDOT:PSS by a layer-by-layer deposition method. Pre-PPV is easily converted to conjugated PPV polymer by a thermal treatment. The CdS nanoparticles-(PPV/PEDOT:PSS) multilayer films constitute efficient acceptor-sensitizer dyad systems, which generate a photocurrent of 2,660 nA/cm2 under the air mass (AM) 1.5 conditions (I=100 mW/cm2) for sample with 4.5 bilayers.

Prenatally diagnosed ectrodactyly at 16 weeks' gestation by 2- and 3-dimensional ultrasonography: a case report.

OBJECTIVE: Ectrodactyly is a rare malformation with various presentations. The current report describes a case of ectrodactyly detected using 2-dimensional (2D) and 3-dimensional (3D) ultrasonography at 16 weeks' gestation. METHODS AND RESULTS: The 2D ultrasonographic findings were ectrodactyly in the right hand and monodactyly in the left hand, and these results were confirmed and further clarified using 3D imaging. The postmortem X-ray findings were consistent with the ultrasonography. CONCLUSION: We conclude that 3D ultrasonography can assist in clarifying 2D ultrasonography findings of hand malformations during the second trimester of pregnancy.

Epigenetic silencing of miR-1271 enhances MEK1 and TEAD4 expression in gastric cancer.

Epigenetic dysregulation is a major driver of tumorigenesis. To identify tumor-suppressive microRNAs repressed by DNA methylation in gastric cancer (GC), we analyzed the genome-wide DNA methylation and microRNA expression profiles of EpCAM+/CD44+ GC cells. Among the set of microRNAs screened, miR-1271 was identified as a microRNA repressed by DNA methylation in GC. Forced miR-1271 expression substantially suppressed the growth, migration, and invasion of GC cells. To identify candidate target genes and signaling pathways regulated by miR-1271, we performed RNA sequencing. Among the genes down-regulated by miR-1271, MAP2K1 (MEK1) was significantly repressed by miR-1271, and the associated ERK/MAPK signaling pathway was also inhibited. TEAD4 was also repressed by miR-1271, and the associated YAP1 signatures within genes regulated by miR-1271 were significantly enriched. These findings uncovered MEK1 and TEAD4 as novel miR-1271 targets and suggest that the epigenetic silencing of miR-1271 is crucial for GC development.