Metabolomics study on improvement effects of Cirsium japonicum extract on hypercholesterolemia model mice / 中国药房

OBJECTIVE To explore the mechanism of Cirsium japonicum extract in improving hypercholesterolemia based on metabolomics technology. METHODS The extract of C. japonicum was prepared by macroporous resin adsorption， and its main components were identified by liquid chromatography-tandem mass spectrometry. The experimental mice were randomly divided into control group （n＝6） and modeling group （n＝16）. The hypercholesterolemia model was induced by diet in modeling group； after modeling， the rats of modeling group were divided into model group （n＝8） and C. japonicum extract group （n＝8）. C. japonicum extract group was given C. japonicum extract 400 mg/（kg·d） by gavage （calculated by extract）， and other 2 groups were given constant volume of 0.3% sodium carboxymethyl cellulose solution， for 6 weeks. After medication， the intervention effect of C. japonicum extract was evaluated by the levels of serum total cholesterol （TC）， triglyceride （TG） and the histopathological changes of liver. The mechanism of C. japonicum extract in improving hypercholesterolemia model mice was investigated by metabolomics. RESULTS It was identified that C. japonicum extract contained 12 components， such as 030302005） chlorogenic acid， linarin and pectolinarin. After 6 weeks of intervention， compared with control group， serum level of TC was increased significantly while the level of TG was decreased significantly in model group （P＜0.05）， while a large number of lipid droplets， disorderly arrangement of liver cells and the damaged structure of liver cord were observed in liver tissue. Compared with model group， the serum level of TC was decreased significantly in C. japonicum extract group（P＜0.05）； the lipid droplets in liver tissue were significantly reduced， with liver cells arranged radially and tightly centered around the central vein， and liver cords arranged neatly. The metabolomics study showed that after the intervention of C. japonicum extract， the levels of metabolites were significantly adjusted back， such as ethanolamine， fumaric acid and cholesterol； finally， three metabolism pathways， such as alanine-aspartate-glutamic acid metabolism， arginine biosynthesis， citric acid cycle， were obtained. CONCLUSIONS The main components of C. japonicum extract are phenolic acids and flavonoids， such as chlorogenic acid， linarin， pectolinarin. C. japonicum extract can improve hypercholesterolemia by regulating the contents and distribution of differential metabolites， adjusting alanine-aspartate-glutamic acid metabolism， arginine biosynthesis and citric acid cycle， participating in oxidation-reduction reaction， improving liver lipid accumulation， and playing anti-inflammatory role.

Reprogramming of Glucose Metabolism Pathways in Triple-negative Breast Cancer Cells under Hypoxia / 中国生物化学与分子生物学报

Metabolic changes are recognized as one of the hallmarks of cancer cells. Previous studies have shown that hypoxia can change the glucose metabolism of cancer cells. However, the mechanisms still need to be studied in detail. In this study, by using RNA-Sequencing (RNA-seq) and bioinformatics analysis, we found that there is a significant change in the expression of 334 genes in BT549 cells and 215 genes in MDA-MB-231 cells induced by hypoxia at the mRNA level. Most of these genes were associated with glucose metabolism. RNA-seq data, Western blot, enzyme activity assays, and metabolite quantification experiments showed that the glucose uptake increased by elevating the expression of glucose transporter protein 1 (GLUT1) in BT549 cells and GLUT1 and GLUT3 in MDA-MB-231 cells induced by hypoxia. Hypoxia promotes glycolysis by increasing the expression of at least one isozyme or enzyme protein subunit of the enzymes that catalyze the each reaction in the glycolysis pathway, as well as the regulatory enzymes 6-phosphofructo-2-kinase/fructose-2, 6-biphosphatase 3 (PFKFB3) and 4 (PFKFB4) isozymes. Hypoxia increases the expression of pyruvate dehydrogenase kinase 1 (PDK1) and PDK3 and reduces the expression of isocitrate dehydrogenase 3(IDH3), succinate dehydrogenase subunit B(SDHB) and D(SDHD) to reduce the aerobic oxidation pathway. The expression of glucose-6-phosphate dehydrogenase (G6PD) and glycogen synthase was significantly increased to promote the pentose phosphate pathway and glycogen synthesis pathway. The mRNA levels of enzyme genes had no significant difference in gluconeogenesis and glycogenolysis. The breast cancer database suggests that the mRNA levels of the glucose metabolism enzymes were consistent in vivo and in vitro. Hypoxia regulates the reprogramming of glucose metabolism by altering the gene expression of isozymes or subunits of these enzymes. The study comprehensively analyzed the effects of hypoxia on the expression of all enzyme genes and major regulatory enzymes in six glucose metabolism pathways and provides an understanding of glucose metabolism in cancer cells under a hypoxia environment.

Transcriptome analysis and validation of key genes involved in biosynthesis of iridoids in Gentiana lhassica / 中国中药杂志

As the main chemical constituents, iridoids are widely distributed within Gentiana, Gentianaceae, with promising bioactivities. Based on the previous work, the transcriptome of G. lhassica, an original plant of Tibetan herb "Jieji Nabao", was sequenced and analyzed in this study, and the transcriptome databases of roots, stems, leaves, and flowers were constructed so as to explore unigenes that may encode the key enzymes in the biosynthetic pathway of iridoids. Then, qRT-PCR was used to validate the relative expression levels of 11 genes named AACT, DXS, MCS, HDS, IDI, GPPS, GES, G10H, 7-DLNGT, 7-DLGT, and SLS in roots, stems, leaves, and flowers. Also, the total contents of gentiopicroside and loganic acid were determined by HPLC, respectively. The results are as follows:(1)a total of 76 486 unigenes with an average length of 852 bp were obtained;(2)335 unigenes were involved in 19 stan-dard secondary metabolism pathways in KEGG database, with phenylpropanoid biosynthesis having the maximum number(75 unigenes), and no isoflavone biosynthetic pathway was annotated;(3)171 unigenes participatedin 27 key enzymes encoding in the biosynthetic pathway of iridoids, and 1-deoxy-D-xylulose-5-phosphate reductoisomerase(DXR) gene was highly expressed;(4)qRT-PCR results were approximately consistent with RNA-Seq data and the relative expression levels of the 11 genes were higher in the aboveground parts(stem, leaf, and flower) than in the underground part(root);(5)the total contents of gentiopicroside and loganic acid were higher in the aboveground parts(stem, leaf, and flower) than in the underground part(root), and the difference was significant. This study provides basic scientific data for accurate species identification, evaluation of germplasm resources, research on secondary pro-duct accumulation of medicinal plants within Gentianaceae, and protection of endangered alpine species.

Transcriptome analysis and exploration of genes involved in the biosynthesis of iridoids in Gentiana crassicaulis (Gentianaceae) / 药学学报

italic>Gentiana crassicaulis Duthie ex Burk. in Gentiana (Sect. Cruciata), Gentianaceae, is one of the original plants of both Gentianae Macrophyllae Radix and Tibetan herb Jie-Ji Na-Bao, which contain such bioactive iridoids as gentiopicroside, loganic acid and others. In this study, based on previous work, the transcriptome of G. crassicaulis was sequenced and analyzed to construct transcriptome databases of roots, stems, leaves and flowers. qRT-PCR verification was conducted for parts of unigenes that may be key enzymes in the pathway of iridoid biosynthesis. The results are as follows: ① a total of 159 534 unigenes were obtained, with an average length of 679 bp. According to the functional classification of GO, unigenes can be divided into 3 categories with 67 branches. The unigenes were aligned in the KOG database and were classified into 25 categories according to function. ② In the KEGG database, 215 unigenes were implicated in 20 standard secondary metabolism pathways. The analysis shows that 305 unigenes encoded 28 key enzymes in the pathway of iridoid biosynthesis, and their expression in different organs is different; and ③ qRT-PCR was approximately consistent with RNA-Seq results. The 7 annotated unigenes identified in this study, HMGS, DXS, MCS, GPPS, G10H, 7-DLNGT and STR, all had higher relative expression levels in the above-ground parts (stem, leaf and flower) than in the underground part (root). Iridoids are common active and index components of such traditional Chinese medicines as Qinjiao, Longdan, Dangyao, and Qingyedan, among others. Therefore, this work provides basic scientific data for further development including obtaining active components or intermediates through biotechnology, exploring the accumulation of effective components, evaluating the quality of different ecotype varieties, and identifying authentic biosynthesis pathways of medicinal materials.

Transcriptomic data analyses of Melicope pteleifolia via Illumina high-throughput sequencing technology / 中草药

Objective: To obtain the transcriptome sequence database of Melicope pteleifolia. Methods: The transcriptome sequencing and systematic bioinformatics analysis were carried out using the second generation high-throughput sequencing platform Illumina HiSeqTM 2000 with mixed root, stem and leaf samples of M. pteleifolia. Results: A total of 47 045 040 high quality sequences (clean reads) were obtained by transcriptome sequencing analysis. A total of 67 956 unigenes were assembled by Trinity de novo, with an average length of 787 nt. BLAST analysis showed that 42 749 (61.92%), 31 152 (45.84%), 26 563 (39.09%), and 17 481 (25.72%) unigenes were annotated in NR, Swiss port, KOG and KEGG databases respectively, and 47 groups were involved in three GO classification: biological process, cellular component and molecular function. A total of 9807 unigenes were annotated to 130 KEGG metabolic pathways, 19 secondary metabolic pathways were screened. Twenty-five different KOG functional groups were obtained by the analysis of KOG functional classification. It was predicted that there were 56 families of higher plant transcription factors. A total of 7 748 simple sequence repeats (SSRs) were found by MISA software. The number (4 117) of the tri-nucleotide SSRs was the richest, with a frequency of 53.1%, and the number of the penta-nucleotide SSRs was relatively small, accounting for 2.2%. Conclusion: The transcriptome information characteristics of root, stem, and leaf of M. pteleifolia can be obtained by high-throughput Illumina sequencing technology and bioinformatics analysis, which will lay a foundation for further research on functional gene mining, secondary metabolic pathway analysis and regulation mechanism of M. pteleifolia.

in vitro Metabolism Pathway of Effective Component of Bletilla striata as Militarine in Liver Microsomes and Kinetics Char- acteristics of Enzyme-catalyzed Reactions / 中国药房

OBJECTIVE： To study in vitro metabolism pathway of effective component of Bletilla striata as Militarine in liver microsomes and kinetics characteristics of enzyme-catalyzed reactions. METHODS： The in vitro incubation system of rat and human liver microsomes was established， and incubation reaction of Militarine was performed. UPLC-QTOF-MS was used to identify the structure of its metabolites in combination with UNIFI database and references. Using puerarin as internal standard， UPLC-Triple Quad-MS was used to quantitatively analyze metabolic transformation of Militarine in rat liver microsomes. The kinetic parameters （vmax， km， CLint） of Militarine enzyme-catalyzed reactions with/without reducing coenzyme Ⅱ （NADPH） were calculated by fitting the curves with GraphPad Prism 5.0 software. RESULTS： After incubation in rat and human liver microsomes， Militarine produced a chemical formula C21H29O11， which was presumed to be a metabolite of Militarine ester bond hydrolysis. The kinetic study of enzyme-catalyzed reactions showed that vmax of Militarine enzyme-catalyzed reactions with/without NADPH were 1.955， 2.129 nmol/（h·mg）； km were 8.601， 9.854 nmol/mL； CLint were 0.227 3， 0.216 1 mL/（h·mg）； there was no significant difference between with NADPH and without NADPH. CONCLUSIONS： The main metabolic pathway of Militarine in liver microsomes is the hydrolysis of C1 and C4 ester bonds. Its metabolism does not depend on the pathway of cytochrome P450 enzymes initiated by NADPH.

Effects of Serglycan on Drug Resistance of Ovarian Cancer and Its Mechanism Based on Bioinformatics / 中国药房

OBJECTIVE： To study the effects of serglycan （SRGN） on drug resistance of ovarian cancer and its mechanism. METHODS： Gene expression profile interactive analysis tool （GEPIA） was used to extract related data set of ovarian cancer and analyze the difference of mRNA expression of SRGN between normal ovary tissue and ovarian cancer tissue. Gene expression database （GEO） was adopted to obtain the difference of the mRNA expression of SRGN in cisplatin sensitive and cisplatin resistant cell lines （A2780）. STRING online database was used to screen proteins interacting with SRGN （confidence degree： 0.900， interactors： 10）. Adopted biological information annotation database （DAVID） to analysis Kyoto encyclopedia of genes and genomers（KEGG）metabolism pathway to predict the potential pathways of SRGN regulating drug resistance of ovarian cancer. Medical ontology information retrieval platform COREMINE was used to mine the biological processes of significant relationship of SRGN and ovarian cancer with drug resistance. RESULTS： mRNA expression of SRGN in ovarian cancer tissue was significantly higher than normal ovarian tissue （P＜0.05）. mRNA expression of SRGN in cisplatin resistant ovarian cancer was significantly higher than cisplatin sensitive ovarian cancer （P＜0.001）. 10 proteins interacting with SRGN were screened， including albumin， transforming growth factor β1， platelet factor 4， fibrinolysin and vascular endothelial growth factor A. SRGN participated in KEGG metabolism pathway of regulating drug resistance of ovarian cancer， including HIF1α pathway， cytokine-cytokine receptor pathway， coagulation and complement cascades pathway， etc. Biological processes included gene expression， cell growth， apoptosis and cell death. CONCLUSION： SRGN mediates drug resistance of ovarian cancer， which is associated with HIF1α signaling pathway and cytokine-cytokine receptor pathway.

Analysis of transcriptomes to explore genes contributing to iridoid biosynthesis in Gentiana waltonii and Gentiana robusta (Gentianaceae) / 药学学报

The roots and flowers of Gentiana waltonii and Gentiana robusta are used as Tibetan herb Jie-Ji in traditional Tibetan medicine, with iridoids as the main active ingredient and index components. To study the pathway of iridoid biosynthesis, roots, stems, leaves and flowers of G. waltonii and G. robusta were subjected to a high-throughput transcriptomic sequencing analysis by Illumina HiseqXTen. After removing insignificant reads and de novo splicing, 79 455 and 78 466 unigenes were obtained from G. waltonii and G. robusta respectively, with average length as 834 bp and 862 bp. The unigene GO functions could be divided into three categories of 65 branches. The unigenes were aligned in KOG database and were classified into 25 classes according to function. In KEGG database, 315 and 340 unigenes of G. waltonii and G. robusta were implicated in 20 standard secondary metabolic pathways, respectively. Furthermore, 80 and 57 unigenes of the two species were analyzed to encode 24 key enzymes in the pathway related to iridoid biosynthesis. There were differences in gene expression among different organs. Based on sequence data, significant amounts of SSRs, SNPs and InDels were detected in each dataset. This study provides a platform for further development of molecular markers, excavation of functional genes, and research into metabolic pathways and their regulatory mechanism within G. waltonii and G. robusta.

Transcriptomic data analyses of rhizome of Souliea vaginata via Illumina high-throughput sequencing technology / 中草药

Objective To obtain the transcriptome dataset of rhizome of Souliea vaginata Methods Using the high-throughput illumina sequencing platform Illumina HiSeqTM 2000 150PE, a rhizome transcriptome dataset of S. vaginata was obtained, followed by systemic bioinformatics analyses. Results The transcriptome sequencing analyses produced to a great number of 63 322 086 high quality clean reads. Trinity de novo assembling resulted in a total of 52 575 unigenes with an average length of 909 nt. BLAST analysis indicated that 28 842 (accounting for 54.86% of the total unigenes), 10 712 (20.37%), 9 245 (17.58%), and 11 559 (21.99%) unigenes were successfully annotated in the NR, Swiss-port, KOG, and KEGG databases, respectively. GO classification contained the basic three major groups, including biological process, cellular component, and molecular function, and 45 subgroups. Among them126 KEGG standard pathways were designated, of which 17 were defied as the secondary metabolism. Of all unigenes, 2 215 with protein coding sequences were predicted, and 55 families of plant transcription factors were also identified. MISA prediction yielded a number of 4 609 simple sequence repeats (SSRs), among which the tri-nucleotide SSRs were abundant with 2 106 (45.7%), whereas the penta-nucleotide SSRs were relatively less, accounting for 2.9%. Conclusion The transcriptomic characteristics of S.vaginata rhizome were revealed by the high-throughput Illumina sequencing technology along with bioinformatics analyses, which would be of great importance for the functional gene characterization, secondary metabolism pathway dissections, and their regulatory mechanisms in S. vaginata.

High-throughput transcriptome sequencing of roots of Dictamnus dasycarpus and data analyses / 中草药

Objective To obtain the transcriptome dataset of roots of Dictamnus dasycarpus. Methods The root transcriptome dataset of D. dasycarpus was obtained using the high-throughput sequencing platform Illumina HiSeqTM 2000 150PE, followed by systemic bioinformatics analyses. Results A great number of 69 643 286 high quality clean reads were obtained by the transcriptome sequencing analyses. Using Trinity de novo assembling, a total of 49 050 unigenes were finally obtained, with an average length of 841 nt. BLAST analysis indicated that 31 636 (accounting 64.49% of the total unigenes), 22 367 (45.60%), 19 246 (39.23%), 12 595 (25.68%) unigenes were successfully annotated in the NR, Swiss-port, KOG, and KEGG databases, respectively. And GO classification contained the basic three major groups, including biological process, cellular component, and molecular function with 42 subgroups. A total of 132 KEGG standard metabolic pathways were designated, 18 of which were defied as the secondary metabolism. Further analysis revealed that a total of 90 unigenes were involved in the biosynthesis of various alkaloids. Of all unigenes, 1 908 were predicted to have CDS, and 55 families of plant transcription factors were also identified. Using MISA prediction, 4 579 simple sequence repeats (SSRs) were obtained, among which the tri-nucleotide SSRs were abundant with 2 021 (44.1%), whereas the penta-nucleotide SSRs accounted for 3.5%. Conclusion The root transcriptome of D. dasycarpus revealed by the high-throughput sequencing technology will be important for gene functional characterization, secondary metabolism pathway exploration, and regulation mechanism research in this species.

High-throughput transcriptomic sequencing of Rheum palmatum L. seedlings and elucidation of genes in anthraquinone biosynthesis / 药学学报

Anthraquinones are not only the main active constituents but also the index components for the quality control of Rhei Radix et Rhizoma. To study the anthraquinone biosynthesis, Rheum palmatum L. seedlings were subjected to a high-throughput transcriptomic sequencing analysis by Illumina HiSeqTM 2000 150PE. The Illumina sequencing generated a total of 11.04 G clean data resulting in 736 309 74 clean reads, deposited in the sequence read archive (SRA accession SRP160030). Trinity do novo assembly yielded 93 646 unigenes, with an average of 1 108 nt. Functional annotation revealed that all unigenes were successfully annotated in the NR, NT, Swiss-port, PFAM, and KOG databases. GO enrichments showed that 57 subgroups were involved in biological process, cellular component, and molecular function. KEGG analysis indicated that 1 107 unigenes were implicated in 19 standard secondary metabolic pathways. 172 unigenes were analyzed to encode 28 key enzymes during the MVA, MEP, shikimic acid, and polyketide pathways related to anthraquinone biosynthesis. 125 CYP450 and 73 UGTs unigenes were related the modification of secondary metabolites in R. palmatum L. Furthermore, seven unigenes with full length cDNAs were successfully verified by RT-PCR and sequencing analyses. Then, MISA prediction produced a number of 18 885 simple sequence repeats (SSRs). Herein, the transcriptomic gene expression profiles of R. palmatum L. and candidate genes during the anthraquinone biosynthesis pathway were obtained for the first time. The results provided basic information for subsequent gene function characterization, secondary metabolic pathway analysis, and anthraquinone biosynthesis and regulation elucidation in R. palmatum L.

Advance in Exercise for Bone Metabolism Pathways (review) / 中国康复理论与实践

The process of exercise regulating bone metabolism is complicated, which involves a number of signaling pathways. A large number of studies in vitro have indicated that mechanical stress regulates bone metabolism by Wnt, bone morphogenetic protein (BMP), and osteoprotegerin (OPG)/receptor activator of NF-κB ligand (RANKL)/receptor activator of NF-κB (RANK) signaling pathways. Both the in-tensity and frequency of mechanical stress have varing impact on bone tissue and cells. Plenty of studies in vivo also have shown that exer-cise regulates bone metabolism by key factors in bone metabolism signaling pathways. This paper reviewed the effects of exercise on bone metabolism pathways and their mechanisms.