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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.
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Productos Biológicos , Medicamentos Herbarios Chinos , Plantas Medicinales , Simulación del Acoplamiento Molecular , Transcriptoma , Productos Biológicos/farmacología , Extractos Vegetales , Medicina Tradicional ChinaRESUMEN
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.
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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.
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Medicamentos Herbarios Chinos , Células Madre Pluripotentes Inducidas , Humanos , Adulto , Células Madre Pluripotentes Inducidas/metabolismo , Medicamentos Herbarios Chinos/farmacología , Etanol/farmacología , Apoptosis , Diferenciación CelularRESUMEN
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.
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Perfilación de la Expresión Génica , Emisiones de Vehículos , Ratones , Animales , Emisiones de Vehículos/toxicidad , Material Particulado/toxicidad , Transcriptoma , Inflamación/inducido químicamente , Inflamación/genéticaRESUMEN
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.
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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.
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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.
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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.
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Antineoplásicos Fitogénicos/farmacología , Perfilación de la Expresión Génica/métodos , Neoplasias Pulmonares/patología , Paeonia/química , Extractos Vegetales/farmacología , Células A549 , Aurora Quinasa B/metabolismo , Humanos , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/metabolismo , Ácido Oleanólico/análogos & derivados , Ácido Oleanólico/metabolismo , Raíces de Plantas/químicaRESUMEN
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.
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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.
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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.
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Antiasmáticos/farmacología , Brassicaceae/química , Epigénesis Genética/efectos de los fármacos , Extractos Vegetales/farmacología , Semillas/química , Animales , Antiasmáticos/química , Asma/tratamiento farmacológico , Asma/inmunología , Asma/patología , Biología Computacional/métodos , Metilación de ADN , Modelos Animales de Enfermedad , Perfilación de la Expresión Génica , Redes Reguladoras de Genes , Ratones , Ovalbúmina/efectos adversos , Ovalbúmina/inmunología , Extractos Vegetales/química , TranscriptomaRESUMEN
The rock bream (Oplegnathus fasciatus) is one of the most economically valuable marine fish in East Asia, and due to various environmental factors, there is substantial revenue loss in the production sector. Therefore, knowledge of its genome is required to uncover the genetic factors and the solutions to these problems. In this study, we constructed the first draft genome of O. fasciatus as a reference for the family Oplegnathidae. The genome size is estimated to be 749 Mb, and it was assembled into 766 Mb by combining Illumina and PacBio sequences. A total of 24,053 transcripts (23,338 genes) are predicted, and among those transcripts, 23,362 (97%), are annotated with functional terms. Finally, the completeness of the genome assembly was assessed by CEGMA, which resulted in the complete mapping of 220 (88.7%) core genes in the genome. To the best of our knowledge, this is the first draft genome for the family Oplegnathidae.
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Genoma , Perciformes/genética , AnimalesRESUMEN
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.
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SLIT has been suggested as a key regulator of cancer development and a promising therapeutic target for cancer treatment. Herein, we analyzed expression and methylation of SLIT1/SLIT2/SLIT3 in 11 gastric cancer cell lines, 96 paired gastric tumors and adjacent normal gastric tissues, and 250 gastric cancers provided by The Cancer Genome Atlas. Methylation of SLIT1/SLIT2/SLIT3 was found both in early gastric cancers, and in advanced gastric cancers. Even normal gastric tissue showed increased methylation of SLIT1 and SLIT3 that correlated with patient age. Furthermore, epigenetic inactivation of SLIT occurred in a gastric cancer subtype-dependent manner. SLIT2 and SLIT3 expression was reduced in Epstein-Barr virus-positive and microsatellite instability subtypes, but increased in the genomically stable subtype. Expression of miR218 correlated negatively with methylation of SLIT2 or SLIT3. These findings suggest that a molecular subtype-specific therapeutic strategy is needed for targeting SLITs and miR-218 in treatment of gastric cancer.
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Expresión Génica , Péptidos y Proteínas de Señalización Intercelular/genética , Proteínas de la Membrana/genética , MicroARNs/genética , Proteínas del Tejido Nervioso/genética , Neoplasias Gástricas/patología , Adulto , Factores de Edad , Anciano , Anciano de 80 o más Años , Línea Celular Tumoral , Metilación de ADN , Regulación hacia Abajo , Epigénesis Genética , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Humanos , Persona de Mediana Edad , Análisis de Secuencia de ADN , Neoplasias Gástricas/genéticaRESUMEN
Abnormal DNA methylation is an epigenetic mechanism that promotes gastric carcinogenesis. While the abnormal methylation at promoter regions has been characterized for many genes, the function of DNA methylation marks at distal regulatory regions in gastric cancer remains poorly described. Here, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines to understand the epigenetic changes in the distal as well as the proximal regulatory regions. In total, 257,651 significant DMRs (Differentially methylated regions) were identified in gastric cancer, and the majority of these DMRs were located in the intergenic, intronic, and non-coding RNA regions. We identified the aberrant expression of many genes and lncRNAs due to changes in DNA methylation. Furthermore, we profiled the molecular subtype-specific methylation patterns in gastric cancer to characterize subtype-specific regulators that undergo DNA methylation changes. Our findings provide insights for understanding methylation changes at distal regulatory regions and reveal novel epigenetic targets in gastric cancer.
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Metilación de ADN/genética , Elementos de Facilitación Genéticos/genética , Regiones Promotoras Genéticas/genética , Neoplasias Gástricas/genética , Epigenómica , HumanosRESUMEN
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.
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Diferenciación Celular , MicroARNs/metabolismo , Desarrollo de Músculos/genética , Músculo Esquelético/fisiología , Mioblastos/citología , Regeneración/genética , Proteína Smad4/genética , Regiones no Traducidas 3' , Animales , Línea Celular , Senescencia Celular , Regulación del Desarrollo de la Expresión Génica , Técnicas de Silenciamiento del Gen , Humanos , Ratones , Ratones Endogámicos C57BL , MicroARNs/genética , Músculo Esquelético/citología , Unión ProteicaRESUMEN
Various types of histone methylation have been associated with cancer progression. Depending on the methylation site in histone proteins, its effects on transcription are different. DPY30 is a common member of SET1/MLL histone H3K4 methyltransferase complexes. However, its expression and roles in gastric cancer have been poorly characterized. To determine whether DPY30 has pathophysiological roles in gastric cancer, its expression and roles were examined. Immunohistochemistry and real time PCR showed up-regulation of DPY30 expression in some gastric cancer cell lines and patients' tissues. Its knockdown by siRNA decreased the proliferation, migration, and invasion of gastric cancer cells, whereas its overexpression showed the opposite effects. These results indicate that DPY30 has critical roles in the proliferation, migration, and invasion of gastric cancer cells, and suggest DPY30 might be a therapeutic target in gastric cancer.
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Movimiento Celular/fisiología , Proliferación Celular/fisiología , Proteínas Nucleares/fisiología , Neoplasias Gástricas/patología , Línea Celular Tumoral , Humanos , Proteínas Nucleares/metabolismo , Neoplasias Gástricas/metabolismo , Factores de TranscripciónRESUMEN
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.