1
|
Li W, Yuan G, Pan Y, Wang C, Chen H. Network Pharmacology Studies on the Bioactive Compounds and Action Mechanisms of Natural Products for the Treatment of Diabetes Mellitus: A Review. Front Pharmacol 2017; 8:74. [PMID: 28280467 PMCID: PMC5322182 DOI: 10.3389/fphar.2017.00074] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/19/2022] Open
Abstract
Diabetes mellitus (DM) is a kind of chronic and metabolic disease, which can cause a number of diseases and severe complications. Network pharmacology approach is introduced to study DM, which can combine the drugs, target proteins and disease and form drug-target-disease networks. Network pharmacology has been widely used in the studies of the bioactive compounds and action mechanisms of natural products for the treatment of DM due to the multi-components, multi-targets, and lower side effects. This review provides a balanced and comprehensive summary on network pharmacology from current studies, highlighting different bioactive constituents, related databases and applications in the investigations on the treatment of DM especially type 2. The mechanisms related to type 2 DM, including α-amylase and α-glucosidase inhibitory, targeting β cell dysfunction, AMPK signal pathway and PI3K/Akt signal pathway are summarized and critiqued. It suggests that the network pharmacology approach cannot only provide a new research paradigm for natural products, but also improve the current antidiabetic drug discovery strategies. Furthermore, we put forward the perspectives on the reasonable applications of network pharmacology for the therapy of DM and related drug discovery.
Collapse
Affiliation(s)
| | | | | | | | - Haixia Chen
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin UniversityTianjin, China
| |
Collapse
|
2
|
Papazian S, Khaling E, Bonnet C, Lassueur S, Reymond P, Moritz T, Blande JD, Albrectsen BR. Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure. PLANT PHYSIOLOGY 2016; 172:2057-2078. [PMID: 27758847 PMCID: PMC5100778 DOI: 10.1104/pp.16.01318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
Plants have evolved adaptive mechanisms that allow them to tolerate a continuous range of abiotic and biotic stressors. Tropospheric ozone (O3), a global anthropogenic pollutant, directly affects living organisms and ecosystems, including plant-herbivore interactions. In this study, we investigate the stress responses of Brassica nigra (wild black mustard) exposed consecutively to O3 and the specialist herbivore Pieris brassicae Transcriptomics and metabolomics data were evaluated using multivariate, correlation, and network analyses for the O3 and herbivory responses. O3 stress symptoms resembled those of senescence and phosphate starvation, while a sequential shift from O3 to herbivory induced characteristic plant defense responses, including a decrease in central metabolism, induction of the jasmonic acid/ethylene pathways, and emission of volatiles. Omics network and pathway analyses predicted a link between glycerol and central energy metabolism that influences the osmotic stress response and stomatal closure. Further physiological measurements confirmed that while O3 stress inhibited photosynthesis and carbon assimilation, sequential herbivory counteracted the initial responses induced by O3, resulting in a phenotype similar to that observed after herbivory alone. This study clarifies the consequences of multiple stress interactions on a plant metabolic system and also illustrates how omics data can be integrated to generate new hypotheses in ecology and plant physiology.
Collapse
Affiliation(s)
- Stefano Papazian
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå (S.P., B.R.A.); Department of Forest Genetic and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden (T.M.)
- Department of Environmental and Biological Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland (E.K., J.D.B.); and
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland (C.B., S.L., P.R.)
| | - Eliezer Khaling
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå (S.P., B.R.A.); Department of Forest Genetic and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden (T.M.)
- Department of Environmental and Biological Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland (E.K., J.D.B.); and
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland (C.B., S.L., P.R.)
| | - Christelle Bonnet
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå (S.P., B.R.A.); Department of Forest Genetic and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden (T.M.)
- Department of Environmental and Biological Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland (E.K., J.D.B.); and
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland (C.B., S.L., P.R.)
| | - Steve Lassueur
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå (S.P., B.R.A.); Department of Forest Genetic and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden (T.M.)
- Department of Environmental and Biological Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland (E.K., J.D.B.); and
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland (C.B., S.L., P.R.)
| | - Philippe Reymond
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå (S.P., B.R.A.); Department of Forest Genetic and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden (T.M.)
- Department of Environmental and Biological Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland (E.K., J.D.B.); and
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland (C.B., S.L., P.R.)
| | - Thomas Moritz
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå (S.P., B.R.A.); Department of Forest Genetic and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden (T.M.)
- Department of Environmental and Biological Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland (E.K., J.D.B.); and
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland (C.B., S.L., P.R.)
| | - James D Blande
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå (S.P., B.R.A.); Department of Forest Genetic and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden (T.M.);
- Department of Environmental and Biological Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland (E.K., J.D.B.); and
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland (C.B., S.L., P.R.)
| | - Benedicte R Albrectsen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå (S.P., B.R.A.); Department of Forest Genetic and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden (T.M.);
- Department of Environmental and Biological Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland (E.K., J.D.B.); and
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland (C.B., S.L., P.R.)
| |
Collapse
|
3
|
Abstract
Embryonic stem (ES) cells have been shown to recapitulate normal developmental stages. They are therefore a highly useful tool in the study of developmental biology. Profiling of ES cell-derived cells has yielded important information about the characteristics of differentiated cells, and allowed the identification of novel marker genes and pathways of differentiation. In this review, we focus on recent results from profiling studies of mouse embryos, human islets, and human ES cell-derived differentiated cells from several research groups. Global gene expression data from mouse embryos have been used to identify novel genes or pathways involved in the developmental process, and to search for transcription factors that regulate direct reprogramming. We introduce gene expression databases of human pancreas cells (Beta Cell Gene Atlas, EuroDia database), and summarize profiling studies of islet- or human ES cell-derived pancreatic cells, with a focus on gene expression, microRNAs, epigenetics, and protein expression. Then, we describe our gene expression profile analyses and our search for novel endoderm, or pancreatic, progenitor marker genes. We differentiated mouse ES cells into mesendoderm, definitive endoderm (DE), mesoderm, ectoderm, and Pdx1-expressing pancreatic lineages, and performed DNA microarray analyses. Genes specifically expressed in DE, and/or in Pdx1-expressing cells, were extracted and their expression patterns in normal embryonic development were studied by in situ hybridization. Out of 54 genes examined, 27 were expressed in the DE of E8.5 mouse embryos, and 15 genes were expressed in distinct domains in the pancreatic buds of E14.5 mouse embryos. Akr1c19, Aebp2, Pbxip1, and Creb3l1 were all novel, and none has been described as being expressed, either in the DE, or in the pancreas. By introducing the profiling results of ES cell-derived cells, the benefits of using ES cells to study early embryonic development will be discussed.
Collapse
Affiliation(s)
- Nobuaki Shiraki
- Department of Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo 2-2-1, Kumamoto 860-0811, Japan
| | - Soichiro Ogaki
- Department of Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo 2-2-1, Kumamoto 860-0811, Japan
| | - Shoen Kume
- Department of Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo 2-2-1, Kumamoto 860-0811, Japan
| |
Collapse
|
4
|
Schweizer F, Fernández-Calvo P, Zander M, Diez-Diaz M, Fonseca S, Glauser G, Lewsey MG, Ecker JR, Solano R, Reymond P. Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior. THE PLANT CELL 2013; 25:3117-32. [PMID: 23943862 PMCID: PMC3784603 DOI: 10.1105/tpc.113.115139] [Citation(s) in RCA: 341] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/18/2013] [Accepted: 07/26/2013] [Indexed: 05/17/2023]
Abstract
Arabidopsis thaliana plants fend off insect attack by constitutive and inducible production of toxic metabolites, such as glucosinolates (GSs). A triple mutant lacking MYC2, MYC3, and MYC4, three basic helix-loop-helix transcription factors that are known to additively control jasmonate-related defense responses, was shown to have a highly reduced expression of GS biosynthesis genes. The myc2 myc3 myc4 (myc234) triple mutant was almost completely devoid of GS and was extremely susceptible to the generalist herbivore Spodoptera littoralis. On the contrary, the specialist Pieris brassicae was unaffected by the presence of GS and preferred to feed on wild-type plants. In addition, lack of GS in myc234 drastically modified S. littoralis feeding behavior. Surprisingly, the expression of MYB factors known to regulate GS biosynthesis genes was not altered in myc234, suggesting that MYC2/MYC3/MYC4 are necessary for direct transcriptional activation of GS biosynthesis genes. To support this, chromatin immunoprecipitation analysis showed that MYC2 binds directly to the promoter of several GS biosynthesis genes in vivo. Furthermore, yeast two-hybrid and pull-down experiments indicated that MYC2/MYC3/MYC4 interact directly with GS-related MYBs. This specific MYC-MYB interaction plays a crucial role in the regulation of defense secondary metabolite production and underlines the importance of GS in shaping plant interactions with adapted and nonadapted herbivores.
Collapse
Affiliation(s)
- Fabian Schweizer
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Patricia Fernández-Calvo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Mark Zander
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Monica Diez-Diaz
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Sandra Fonseca
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Gaétan Glauser
- Chemical Analytical Service of the Swiss Plant Science Web, University of Neuchâtel, 2009 Neuchatel, Switzerland
| | - Mathew G. Lewsey
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Roberto Solano
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
- Address correspondence to
| |
Collapse
|
5
|
Yang Z, Yang J, Liu W, Wu L, Xing L, Wang Y, Fan X, Cheng Y. T2D@ZJU: a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat052. [PMID: 23846596 PMCID: PMC3708620 DOI: 10.1093/database/bat052] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Type 2 diabetes mellitus (T2D), affecting >90% of the diabetic patients, is one of the major threats to human health. A comprehensive understanding of the mechanisms of T2D at molecular level is essential to facilitate the related translational research. Here, we introduce a comprehensive and up-to-date knowledgebase for T2D, i.e. T2D@ZJU. T2D@ZJU contains three levels of heterogeneous connections associated with T2D, which is retrieved from pathway databases, protein-protein interaction databases and literature, respectively. In current release, T2D@ZJU contains 1078 T2D related entities such as proteins, protein complexes, drugs and others together with their corresponding relationships, which include 3069 manually curated connections, 14,893 protein-protein interactions and 26,716 relationships identified by text-mining technology. Moreover, T2D@ZJU provides a user-friendly web interface for users to browse and search data. A Cytoscape Web-based interactive network browser is available to visualize the corresponding network relationships between T2D-related entities. The functionality of T2D@ZJU is shown by means of several case studies. Database URL: http://tcm.zju.edu.cn/t2d.
Collapse
Affiliation(s)
- Zhenzhong Yang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Novel pancreatic endocrine maturation pathways identified by genomic profiling and causal reasoning. PLoS One 2013; 8:e56024. [PMID: 23418498 PMCID: PMC3572136 DOI: 10.1371/journal.pone.0056024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/04/2013] [Indexed: 12/18/2022] Open
Abstract
We have used a previously unavailable model of pancreatic development, derived in vitro from human embryonic stem cells, to capture a time-course of gene, miRNA and histone modification levels in pancreatic endocrine cells. We investigated whether it is possible to better understand, and hence control, the biological pathways leading to pancreatic endocrine formation by analysing this information and combining it with the available scientific literature to generate models using a casual reasoning approach. We show that the embryonic stem cell differentiation protocol is highly reproducible in producing endocrine precursor cells and generates cells that recapitulate many aspects of human embryonic pancreas development, including maturation into functional endocrine cells when transplanted into recipient animals. The availability of whole genome gene and miRNA expression data from the early stages of human pancreatic development will be of great benefit to those in the fields of developmental biology and diabetes research. Our causal reasoning algorithm suggested the involvement of novel gene networks, such as NEUROG3/E2F1/KDM5B and SOCS3/STAT3/IL-6, in endocrine cell development We experimentally investigated the role of the top-ranked prediction by showing that addition of exogenous IL-6 could affect the expression of the endocrine progenitor genes NEUROG3 and NKX2.2.
Collapse
|
7
|
Masclaux FG, Bruessow F, Schweizer F, Gouhier-Darimont C, Keller L, Reymond P. Transcriptome analysis of intraspecific competition in Arabidopsis thaliana reveals organ-specific signatures related to nutrient acquisition and general stress response pathways. BMC PLANT BIOLOGY 2012; 12. [PMID: 23194435 PMCID: PMC3536592 DOI: 10.1186/1471-2229-12-227] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
BACKGROUND Plants are sessile and therefore have to perceive and adjust to changes in their environment. The presence of neighbours leads to a competitive situation where resources and space will be limited. Complex adaptive responses to such situation are poorly understood at the molecular level. RESULTS Using microarrays, we analysed whole-genome expression changes in Arabidopsis thaliana plants subjected to intraspecific competition. The leaf and root transcriptome was strongly altered by competition. Differentially expressed genes were enriched in genes involved in nutrient deficiency (mainly N, P, K), perception of light quality, and responses to abiotic and biotic stresses. Interestingly, performance of the generalist insect Spodoptera littoralis on densely grown plants was significantly reduced, suggesting that plants under competition display enhanced resistance to herbivory. CONCLUSIONS This study provides a comprehensive list of genes whose expression is affected by intraspecific competition in Arabidopsis. The outcome is a unique response that involves genes related to light, nutrient deficiency, abiotic stress, and defence responses.
Collapse
Affiliation(s)
- Frédéric G Masclaux
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, 1015, Switzerland
| | - Friederike Bruessow
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, 1015, Switzerland
- Present address: Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Köln, 50829, Germany
| | - Fabian Schweizer
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, 1015, Switzerland
| | | | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, 1015, Switzerland
| |
Collapse
|