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1.
Brief Bioinform ; 24(6)2023 09 22.
Article in English | MEDLINE | ID: mdl-37798251

ABSTRACT

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.


Subject(s)
Biological Products , Drugs, Chinese Herbal , Plants, Medicinal , Molecular Docking Simulation , Transcriptome , Biological Products/pharmacology , Plant Extracts , Medicine, Chinese Traditional
2.
Genomics ; 115(6): 110710, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37734486

ABSTRACT

DNA-based prediction of externally visible characteristics (EVC) with SNPs is one of the research areas of interest in the forensic field. Based on a previous study performing GWAS on facial traits in a Korean population, herein, we present results stemming from GWA analysis with KoreanChip and novel genetic loci satisfying genome-wide significant level. We discovered a total of 20 signals and 12 loci were found to have novel associations with facial traits, including six loci located in intergenic regions and six loci located at UBE2O, HECTD2, CCDC108, TPK1, FCN2, and FRMPD1. Additionally, we performed a polygenic score analysis for 33 distance-related traits in facial phenotyping and determined genetic relationships between facial traits and SNPs using the GCTA program. The results of the current study offer an understanding of how facial morphology is influenced by complex genetic structures and provide insights into forensic investigation and population genetics.


Subject(s)
Genetic Loci , Genome-Wide Association Study , Humans , Genome-Wide Association Study/methods , Phenotype , Genetics, Population , Republic of Korea , Polymorphism, Single Nucleotide , Ubiquitin-Conjugating Enzymes/genetics
3.
Int J Mol Sci ; 25(18)2024 Sep 23.
Article in English | MEDLINE | ID: mdl-39337710

ABSTRACT

Herbs, such as Aconitum carmichaeli Debeaux (ACD), have long been used as therapies, but it is difficult to identify which organs of the human body are affected by the various compounds. In this study, we predicted the organ where the drug predominantly acts using bioinformatics and verified it using transcriptomics. We constructed a computer-aided brain system network (BSN) and intestinal system network (ISN). We predicted the action points of ACD using network pharmacology (NP) analysis and predicted the dockable proteins acting in the BSN and ISN using statistical-based docking analysis. The predicted results were verified using ACD-induced transcriptome analysis. The predicted results showed that both the NP and docking analyses predominantly acted on the BSN and showed better hit rates in the hub nodes. In addition, we confirmed through verification experiments that the SW1783 cell line had more than 10 times more differentially expressed genes than the HT29 cell line and that the dominant acting organ is the brain, using network dimension spanning analysis. In conclusion, we found that ACD preferentially acts in the brain rather than in the intestine, and this multi-bioinformatics-based approach is expected to be used in future studies of drug efficacy and side effects.


Subject(s)
Aconitum , Computational Biology , Aconitum/chemistry , Humans , Computational Biology/methods , Gene Expression Profiling , Brain/metabolism , Brain/drug effects , Transcriptome/drug effects , Molecular Docking Simulation , Network Pharmacology , Intestines/drug effects , HT29 Cells , Plant Extracts/pharmacology , Plant Extracts/chemistry
4.
BMC Genomics ; 19(1): 481, 2018 Jun 19.
Article in English | MEDLINE | ID: mdl-29921221

ABSTRACT

BACKGROUND: Face morphology is strongly determined by genetic factors. However, only a small number of genes related to face morphology have been identified to date. Here, we performed a two-stage genome-wide association study (GWAS) of 85 face morphological traits in 7569 Koreans (5643 in the discovery set and 1926 in the replication set). RESULTS: In this study, we analyzed 85 facial traits, including facial angles. After discovery GWAS, 128 single nucleotide polymorphisms (SNPs) showing an association of P < 5 × 10- 6 were selected to determine the replication of the associations, and meta-analysis of discovery GWAS and the replication analysis resulted in five genome-wide significant loci. The OSR1-WDR35 [rs7567283, G allele, beta (se) = -0.536 (0.096), P = 2.75 × 10- 8] locus was associated with the facial frontal contour; the HOXD1-MTX2 [rs970797, A allele, beta (se) = 0.015 (0.003), P = 3.97 × 10- 9] and WDR27 [rs3736712, C allele, beta (se) = 0.293 (0.048), P = 8.44 × 10- 10] loci were associated with eye shape; and the SOX9 [rs2193054, C allele, beta (se) (ln-transformed) = -0.007 (0.001), P = 6.17 × 10- 17] and DHX35 [rs2206437, A allele, beta (se) = -0.283 (0.047), P = 1.61 × 10- 9] loci were associated with nose shape. WDR35 and SOX9 were related to known craniofacial malformations, i.e., cranioectodermal dysplasia 2 and campomelic dysplasia, respectively. In addition, we found three independent association signals in the SOX9 locus, and six known loci for nose size and shape were replicated in this study population. Interestingly, four SNPs within these five face morphology-related loci showed discrepancies in allele frequencies among ethnic groups. CONCLUSIONS: We identified five novel face morphology loci that were associated with facial frontal contour, nose shape, and eye shape. Our findings provide useful genetic information for the determination of face morphology.


Subject(s)
Genetic Loci/genetics , Genome-Wide Association Study/methods , Polymorphism, Single Nucleotide/genetics , Aged , Female , Gene Frequency/genetics , Genetic Predisposition to Disease/genetics , Genotype , Homeodomain Proteins/genetics , Humans , Male , Middle Aged , Phenotype , SOX9 Transcription Factor/genetics
5.
Int J Biometeorol ; 62(4): 543-551, 2018 Apr.
Article in English | MEDLINE | ID: mdl-29098422

ABSTRACT

This study was conducted to investigate the effects of chronic and repetitive diving in cold sea water on physiological responses to cold in older Korean female divers, Haenyeo, who have been exposed to cold water through breath-hold diving since their teens. Young and older females, who have no experience of swimming in cold sea water, were recruited as control groups: older haenyeos (N = 10, 70 ± 3 years of age), young non-diving females (N = 10, 23 ± 2 years), and older non-diving females (N = 6, 73 ± 4 years). For the test of cold exposure, all subjects were exposed to cold in an air temperature of 12 °C with 45% RH in a sitting position for 60 min. The changes in core temperature showed no significant differences between older haenyeos and the other two groups. The decreases in mean skin temperature were greater for older haenyeos than the other two groups (P < 0.01). Older haenyeos had significantly lower energy expenditure during cold exposure when compared to older non-diving females (P < 0.05). Heart rate was significantly lower in older haenyeos than that of young non-diving females (P < 0.05). Older haenyeos felt cooler at the face with lower face temperature when compared with older non-diving females. The results indicate that older haenyeos respond to cold through reducing heat loss from the skin rather than increasing metabolic rate. These responses are distinctive features from the cold defensive system of young or older non-diving females.


Subject(s)
Acclimatization/physiology , Aging/physiology , Cold-Shock Response/physiology , Diving/physiology , Adult , Aged , Blood Pressure , Body Temperature , Body Temperature Regulation , Cold Temperature , Energy Metabolism , Female , Heart Rate , Humans , Republic of Korea , Thermosensing , Young Adult
6.
BMC Complement Altern Med ; 17(1): 150, 2017 Mar 09.
Article in English | MEDLINE | ID: mdl-28279166

ABSTRACT

BACKGROUND: In adipose tissues, adipokine levels, including adiponectin and leptin, are involved in insulin sensitivity and are reciprocally induced by cold temperature stress. Thermogenic response in the extremities (hands and feet) against cold stress can be negatively related to fat mass accumulation, particularly in the abdomen. However, the relationship between the sensation of cold in the extremities and circulating levels of adipokines is not fully understood. Here, we investigated whether adipokine levels are associated with cold hypersensitivity in the hands and feet (CHHF), independent of body mass, and whether the CHHF is related to metabolic syndrome (MS). METHODS: Associations of the CHHF with serum levels of adipokines and MS risk were evaluated in 1021 Koreans (372 men and 649 women), using a linear regression model while controlling for thermogenic factors and a logistic regression model, respectively. RESULTS: The adiponectin levels were positively associated with the CHHF, particularly in women, irrespective of thermogenic factors, including body mass index (ß = 1.23 µg/mL, 95% confidence interval [1.04-1.45]). Logistic regression analysis for MS risk via the CHHF showed that there was a significant inverse association in women (odds ratio = 0.449, 95% confidence interval [0.273-0.737]). CONCLUSIONS: In summary, our founding indicated that the CHHF could induce increased levels of circulating adiponectin and in turn reduce the MS risk in women. Despite complaints of feeling cold, these women could be at lower risk of cardiovascular disease.


Subject(s)
Adiponectin/blood , Cryopyrin-Associated Periodic Syndromes , Foot/physiopathology , Hand/physiopathology , Adult , Aged , Cohort Studies , Cryopyrin-Associated Periodic Syndromes/blood , Cryopyrin-Associated Periodic Syndromes/physiopathology , Female , Humans , Male , Metabolic Syndrome/blood , Middle Aged , Republic of Korea , Stress, Physiological/physiology
7.
Int J Biometeorol ; 61(7): 1299-1307, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28160059

ABSTRACT

The aim of the present study was to evaluate the local cold tolerance of older Korean female divers, haenyeo (N = 22) in terms of cold acclimatization and ageing. As control groups, older non-diving females (N = 25) and young females from a rural area (N = 15) and an urban area (N = 51) participated in this study. To evaluate local cold tolerance, finger cold-induced vasodilation (CIVD) during finger immersion of 4 °C water was examined. As a result, older haenyeos showed greater minimum finger temperature and recovery finger temperature than older non-diving females (P < 0.05), but similar responses in onset time, peak time, maximum finger temperature, frequency of CIVD, heart rate, blood pressure, and thermal and pain sensations as those of older non-diving females. Another novel finding was that young urban females showed more vulnerable responses to local cold in CIVD variables and subjective sensations when compared to older females, whereas young rural females had the most excellent cold tolerance in terms of maximum temperature and frequency of CIVD among the four groups (P < 0.05). The present results imply that older haenyeos still retain cold acclimatized features on the periphery even though they changed their cotton diving suits to wet suits in the early 1980s. However, cardiovascular responses and subjective sensations to cold reflect aging effects. In addition, we suggest that young people who have been adapted to highly insulated clothing and indoor heating systems in winter should be distinguished from young people who were exposed to less modern conveniences when compared to the aged in terms of cold tolerance.


Subject(s)
Aging/physiology , Body Temperature Regulation/physiology , Cold Temperature , Diving/physiology , Fingers/physiology , Adult , Aged , Aged, 80 and over , Arterial Pressure , Asian People , Female , Heart Rate , Humans , Pain/physiopathology , Skin Temperature , Thermosensing , Vasodilation/physiology , Young Adult
8.
BMC Complement Altern Med ; 15: 120, 2015 Apr 15.
Article in English | MEDLINE | ID: mdl-25888059

ABSTRACT

BACKGROUND: Body constitutional types described in the traditional Korean medicine system, Sasang constitutional medicine, are heritable, as has been revealed by twin and family studies. Thus, individuals with the same constitution type usually have similar pathophysiological and psychological traits. In several recent genome-wide association (GWA) analyses performed to identify constitution-associated variants, the association signals were not replicated due to small sample size and dissimilar, non-objective methods for classification of the constitutional types. METHODS: We conducted GWA analysis and followed replication analysis in two large populations (5,490 subjects: 3,810 subjects at discovery stage and 1,680 subjects at replication stage) to identify the replicable constitution-associated variants, wherein subjects with the highest tertile of constitution probability values versus the reference with the lowest tertile of the values obtained from a recently developed constitution analysis tool were compared. RESULTS: We found that the obesity-risk variant in intron 1 of the fat mass and obesity-associated (FTO) gene was replicably inversely associated with the So-Eum (SE) type, characterized by reduced appetite, slim body, and cautious personality (rs7193144 in combined samples: odds ratio = 0.729, p = 1.47 × 10(-7)), and substantial association signal remained after controlling for body mass index (BMI). In contrast, the association of the variant with the Tae-Eum type, characterized by high body mass, disappeared after controlling BMI. CONCLUSIONS: In summary, the obesity-risk variant in FTO intron 1 was inversely associated with the SE type, independent of BMI, which corresponded well with the characteristics of the SE type, such as the lowest body mass and lowest susceptibility to metabolic disorders among the constitutional types. Therefore, the obesity-risk variant of FTO associated with body mass increase might be involved in the determination of body constitution type.


Subject(s)
Body Mass Index , Medicine, Korean Traditional , Obesity/genetics , Phenotype , Somatotypes/genetics , Aged , Body Constitution/genetics , Female , Genome-Wide Association Study/methods , Humans , Male , Middle Aged , Risk Factors
9.
Lipids Health Dis ; 13: 45, 2014 Mar 12.
Article in English | MEDLINE | ID: mdl-24618354

ABSTRACT

BACKGROUND: Single-nucleotide polymorphisms (SNPs) around the apolipoprotein A5 gene (APOA5) have pleiotropic effects on the levels of triglyceride (TG) and high-density lipoprotein cholesterol (HDL-C). APOA5 SNPs have also been associated with metabolic syndrome (MS). Here, we constructed haplotypes with SNPs spanning APOA5 and ZNF259, which are approximately 1.3 kb apart, to perform association analyses with the risk for MS and the levels of TG and HDL-C in terms of a TG:HDL-C ratio. METHODS: The effects of three constructed haplotypes (TAA, CGG, and CGA, in the order of rs662799, rs651821, and rs6589566) on the TG:HDL-C ratio and MS were estimated using multiple regression analyses in 2,949 Koreans and in each gender separately (1,082 men and 1,867 women). RESULTS: The haplotypes, CGG and CGA, were associated with the TG:HDL-C ratio and the risk of MS development in both genders. That is, the minor alleles of the rs662799 and rs651821 in APOA5, irrespective of which allele was present at rs6589566, had the marked effects. Interestingly, a C-G-A haplotype at these three SNPs had the most marked effects on the TG:HDL-C ratio and the risk of MS development in women. CONCLUSIONS: We have identified the novel APOA5-ZNF259 haplotype manifesting sex-dependent effects on elevation of the TG:HDL-C ratio as well as the increased risk for MS.


Subject(s)
Apolipoproteins A/genetics , Carrier Proteins/genetics , Cholesterol, HDL/blood , Metabolic Syndrome/genetics , Triglycerides/blood , Adult , Apolipoprotein A-V , Case-Control Studies , Female , Genetic Association Studies , Genetic Predisposition to Disease , Haplotypes , Humans , Linkage Disequilibrium , Male , Membrane Transport Proteins , Metabolic Syndrome/blood , Middle Aged , Polymorphism, Single Nucleotide , Republic of Korea , Risk Factors , Sex Characteristics
10.
BMC Complement Altern Med ; 14: 230, 2014 Jul 09.
Article in English | MEDLINE | ID: mdl-25005712

ABSTRACT

BACKGROUND: Abnormal lipid concentrations are risk factors for atherosclerosis and cardiovascular disease. The pathological susceptibility to cardiovascular disease risks such as metabolic syndrome, diabetes mellitus, hypertension, insulin resistance, and so on differs between Sasang constitutional types. METHODS: We used multiple regression analyses to study the association between lipid-related traits and genetic variants from several genome-wide association studies according to Sasang constitutional types, considering that the Tae-Eum (TE) has predominant cardiovascular risk. RESULTS: By analyzing 26 variants of 20 loci in two Korean populations (8,597 subjects), we found that 12 and 5 variants, respectively, were replicably associated with lipid levels and dyslipidemia risk. By analyzing TE and non-TE type (each 2,664 subjects) populations classified on the basis of Sasang constitutional medicine, we found that the minor allele effects of three variants enriched in TE type had a harmful influence on lipid risk (near apolipoprotein A-V (APOA5)-APOA4-APOC3-APOA1 on increased triglyceride: p = 8.90 × 10(-11), in APOE-APOC1-APOC4 on increased low-density lipoprotein cholesterol: p = 1.63 × 10(-5), and near endothelial lipase gene on decreased high-density lipoprotein cholesterol: p = 4.28 × 10(-3)), whereas those of three variants (near angiopoietin-like 3 gene, APOA5-APOA4-APOC3-APOA1, and near lipoprotein lipase gene on triglyceride and high-density lipoprotein cholesterol) associated in non-TE type had neutral influences because of a compensating effect. CONCLUSIONS: These results implied that the minor allele effects of lipid-associated variants may predispose TE type subjects to high cardiovascular disease risk because of their genetic susceptibility to lipid-related disorders.


Subject(s)
Cardiovascular Diseases/genetics , Genetic Loci , Lipid Metabolism/genetics , Lipids/blood , Lipids/genetics , Adult , Asian People/genetics , Cardiovascular Diseases/blood , Dyslipidemias/genetics , Female , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Male , Middle Aged , Polymorphism, Single Nucleotide , Regression Analysis , Republic of Korea , Risk Factors
11.
Phytomedicine ; 123: 155057, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37984121

ABSTRACT

BACKGROUND: Although chronic treatment with glucocorticoids, such as dexamethasone, is frequently associated with muscle atrophy, effective and safe therapeutics for treating muscle atrophy remain elusive. Jakyak-gamcho-tang (JGT), a decoction of Paeoniae Radix and Glycyrrhizae Radix et Rhizoma, has long been used to relieve muscle tension and control muscle cramp-related pain. However, the effects of JGT on glucocorticoid-induced muscle atrophy are yet to be comprehensively clarified. PURPOSE: The objective of the current study was to validate the protective effect of JGT in dexamethasone-induced muscle atrophy models and elucidate its underlying mechanism through integrated in silico - in vitro - in vivo studies. STUDY DESIGN AND METHODS: Differential gene expression was preliminarily analyzed using the RNA-seq data to determine the effects of JGT on C2C12 myotubes. The protective effects of JGT were further validated in dexamethasone-treated C2C12 myotubes by assessing cell viability, myotube integrity, and mitochondrial function or in C57BL/6 N male mice with dexamethasone-induced muscle atrophy by evaluating muscle mass and physical performance. Transcriptomic pathway analysis was also performed to elucidate the underlying mechanism. RESULTS: Based on preliminary gene set enrichment analysis using the RNA-seq data, JGT regulated various pathways related to muscle differentiation and regeneration. Dexamethasone-treated C2C12 myotubes and muscle tissues of atrophic mice displayed substantial muscle protein degradation and muscle loss, respectively, which was efficiently alleviated by JGT treatment. Importantly, JGT-mediated protective effects were associated with observations such as preservation of mitochondrial function, upregulation of myogenic signaling pathways, including protein kinase B/mammalian target of rapamycin/forkhead box O3, inhibition of ubiquitin-mediated muscle protein breakdown, and downregulation of inflammatory and apoptotic pathways induced by dexamethasone. CONCLUSION: To the best of our knowledge, this is the first report to demonstrate that JGT could be a potential pharmaceutical candidate to prevent muscle atrophy induced by chronic glucocorticoid treatment, highlighting its known effects for relieving muscle spasms and pain. Moreover, transcriptomic pathway analysis can be employed as an efficient in silico tool to predict novel pharmacological candidates and elucidate molecular mechanisms underlying the effects of herbal medications comprising diverse biologically active ingredients.


Subject(s)
Drugs, Chinese Herbal , Glucocorticoids , Glycyrrhiza , Paeonia , Male , Mice , Animals , Mice, Inbred C57BL , Muscular Atrophy/chemically induced , Muscular Atrophy/drug therapy , Muscle Fibers, Skeletal , Muscle Proteins/metabolism , Muscle Proteins/pharmacology , Muscle Proteins/therapeutic use , Dexamethasone/pharmacology , Pain , Mammals
12.
Sci Data ; 11(1): 974, 2024 Sep 06.
Article in English | MEDLINE | ID: mdl-39242618

ABSTRACT

Traditional herbal medicine, rooted in a long history of use in East Asia, combines several herbs to create treatments showing high efficacy with minimal side effects, for specific diseases. Such combination therapies represent a potential reservoir of new drugs for treating multifactorial and incurable chronic diseases. However, the complexity of their mechanisms of action due to the combination of multiple compounds, has limited their research integration into modern pharmacological science. To address this challenge, we constructed drug-induced transcriptome data for herbal medicines through systematic experiments, analyzed with the aid of various omics databases. We introduce KORE-Map 1.0 (Korean medicine Omics Resource Extension Map), the first comprehensive resource of drug-derived transcriptome data for representative tonifying herbal medicines, effective in enhancing the immune system. This dataset aims to provide novel insights into the combinatorial mechanisms of these herbal medicines and to aid in the discovery of new therapeutic targets and indications for various incurable diseases.


Subject(s)
Transcriptome , Humans , Medicine, Korean Traditional , Plants, Medicinal/genetics , Herbal Medicine
13.
Forensic Sci Res ; 8(1): 62-69, 2023 Mar.
Article in English | MEDLINE | ID: mdl-37415797

ABSTRACT

Human face is a highly heritable and complex trait. Many genome-wide analyses have identified genetic variants influencing facial morphology. Genome-wide association studies (GWASs) investigating facial morphologies of different populations provide a comprehensive insight into the genetic basis of the human face. Here, we report a GWAS of normal facial variation in Koreans using an array optimized for the Korean population (KoreanChip). We found that novel genetic variants encompassing four loci reached the genome-wide significance threshold. They include LOC107984547, UBE2O, TPK1, and LINC01148 loci associated with facial angle, brow ridge protrusion, nasal height, and eyelid curvature. Our results also validated previously published genetic loci, including FAT4, SOX9, and TBX3 loci. All confirmed genetic variants showed phenotypic differences involving each facial trait based on the effect of the minor allele. The present study highlights genetic signals associated with normal human facial variation and provides candidates for functional studies. Key points: GWAS of normal facial variation in the Korean population was conducted using a Korean genome chip.Previously reported genetic signals associated with FAT4, SOX9, and TBX3 loci were replicated in the Korean populations.Genetic signals in UBE2O and TPK1 loci were identified as novel variants for corresponding facial features.

14.
Article in English | MEDLINE | ID: mdl-21860654

ABSTRACT

Apolipoprotein A5 (APOA5) was identified as a strong modulator of serum lipids. Moreover, an APOA5 gene -1131T>C polymorphism has been associated with serum lipids, but the results are inconsistent according to ethnic and racial groups. We have genotyped and analyzed 1,619 outpatients of Korean oriental medicine hospitals who were classified into three Sasang constitution groups (SCGs), So-Yang (SY), So-Eum (SE), and Tae-Eum (TE). There were no significant difference in the distribution of the APOA5 -1131T>C genotype among the three SCGs. Subjects with the C allele in SY and TE showed significantly lower serum high-density lipoprotein cholesterol (HDL-C) and higher triglyceride (TG) levels than noncarriers of the C allele. These results show the differences in the prevalence of decreasing serum HDL-C and elevating serum TG levels along with APOA5 -1131T>C polymorphism according to SCG and suggest that SCG may act as a significant risk factor for hypo-HDL-C-emia and hypertriglyceridemia susceptibility.

15.
Plants (Basel) ; 11(7)2022 Apr 06.
Article in English | MEDLINE | ID: mdl-35406976

ABSTRACT

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.

16.
BMB Rep ; 55(9): 417-428, 2022 Sep.
Article in English | MEDLINE | ID: mdl-35880436

ABSTRACT

Herbal medicine, a multi-component treatment, has been extensively practiced for treating various symptoms and diseases. However, its molecular mechanism of action on the human body is unknown, which impedes the development and application of herbal medicine. To address this, recent studies are increasingly adopting systems pharmacology, which interprets pharmacological effects of drugs from consequences of the interaction networks that drugs might have. Most conventional network- based approaches collect associations of herb-compound, compound-target, and target-disease from individual databases, respectively, and construct an integrated network of herb-compound- target-disease to study the complex mechanisms underlying herbal treatment. More recently, rapid advances in highthroughput omics technology have led numerous studies to exploring gene expression profiles induced by herbal treatments to elicit information on direct associations between herbs and genes at the genome-wide scale. In this review, we summarize key databases and computational methods utilized in systems pharmacology for studying herbal medicine. We also highlight recent studies that identify modes of action or novel indications of herbal medicine by harnessing drug-induced transcriptome data. [BMB Reports 2022; 55(9): 417-428].


Subject(s)
Drugs, Chinese Herbal , Herbal Medicine , Drugs, Chinese Herbal/pharmacology , Humans , Network Pharmacology , Phytotherapy , Transcriptome
17.
Front Pharmacol ; 13: 1010520, 2022.
Article in English | MEDLINE | ID: mdl-36304143

ABSTRACT

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.

18.
Biomed Pharmacother ; 148: 112748, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35219117

ABSTRACT

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.


Subject(s)
Antineoplastic Agents, Phytogenic/pharmacology , Gene Expression Profiling/methods , Lung Neoplasms/pathology , Paeonia/chemistry , Plant Extracts/pharmacology , A549 Cells , Aurora Kinase B/metabolism , Humans , Lung Neoplasms/drug therapy , Lung Neoplasms/metabolism , Oleanolic Acid/analogs & derivatives , Oleanolic Acid/metabolism , Plant Roots/chemistry
19.
Integr Med Res ; 11(1): 100752, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34345586

ABSTRACT

BACKGROUND: Skin aging is caused by exogenous and endogenous factors and is commonly manifested as wrinkling, sagging, and looseness of the skin. The herbal extract including Zingiber officinale Roscoe, Atractylodes chinensis (Bunge) Kodiz, Curcuma longa L., and Cinnamomum cassia (L.) J.Presl (ZACC extract), is widely used for So-eum (SE) Sasang constitutional type individuals. This study aimed to examine the protective effects of the ZACC extract against skin aging in 21 SE type subjects. METHODS: The safety and clinical efficacy of herbal cream were evaluated after application on human skin in a split-face randomized, double-blind, placebo-controlled study. The Sasang Constitution Analysis Tool (SCAT) was used to select 21 SE type subjects, who applied herbal cream and placebo cream for 12 weeks. Visual assessment, wrinkle parameters, questionnaires, and skin safety were evaluated. RESULTS: The visual assessment score was decreased by using of the herbal cream, but there were no significant differences between groups. Among the wrinkle parameters, R1 (skin roughness) and R4 (smoothness depth) values were significantly improved after the application of the herbal cream compared to those observed after application of the placebo cream for 12 weeks. No significant differences were observed in evaluation of the product efficacy and usability by questionnaires. There were no adverse dermatologic reactions in the SE type subjects during the evaluation period. CONCLUSION: The ZACC herbal cream may be used to prevent or slow skin aging, including wrinkle formation, in SE type individuals.

20.
Article in English | MEDLINE | ID: mdl-19822564

ABSTRACT

Sasang constitutional medicine (SCM), a Korean tailored medicine, categorizes human beings into four types through states of physiological imbalances and responsiveness to herbal medicine. One SCM type susceptible to obesity seems sensitive to energy intake due to an imbalance toward preserving energy. Common variants of fat mass and obesity associated (FTO) and melanocortin 4 receptor (MC4R) genes have been associated with increased body mass index (BMI) by affecting energy intake. Here, we statistically examined the association of FTO and MC4R polymorphisms with BMI in two populations with 1370 Koreans before and after SCM typing, and with the lowering of BMI in 538 individuals who underwent a 1-month lifestyle intervention. The increased BMI replicated the association with FTO haplotypes (effect size ≃ 1.1 kg/m(2)) and MC4R variants (effect size ≃ 0.64 kg/m(2)). After the lifestyle intervention, the carriers of the haplotype represented by the minor allele of rs1075440 had a tendency to lose more waist-to-hip ratio (0.76%) than non-carriers. The constitutional discrepancy for the accumulation of body mass by the effects of FTO and/or MC4R variants seemed to reflect the physique differences shown in each group of SCM constitutional types. In conclusion, FTO and MC4R polymorphisms appear to play an important role in weight gain, while only FTO variants play a role in weight loss after lifestyle intervention. Different trends were observed among individuals of SCM types, especially for weight gain. Therefore, classification of individuals based on physiological imbalance would offer a good genetic stratification system in assessing the effects of obesity genes.

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