环境污染物发育毒性机制研究的系统生物学方法进展Review of Systems Biology Approach to Study on Developmental Toxicity Mechanism of Environmental Pollutants
徐挺;赵静;胡霞林;尹大强;
摘要(Abstract):
基因调控网络(gene regulatory network,GRN)是用于研究基因调控的一种新兴的系统生物学方法,尤其适合描述生物体早期发育的调控系统和机制。由于它能体现出调控过程的网络特性和动态关系,从整体的角度全面审视环境扰动所造成的真实影响,因此有望在内分泌干扰物等环境污染物的发育毒性机制研究中发挥重要作用,解决多年来一直困扰相关研究的种种难题。针对基因调控网络的结构、研究方法、应用成果和案例进行综述,并对将这一方法应用于污染物发育毒性机制研究的前景做出展望。
关键词(KeyWords): 基因调控网络;内分泌干扰物;发育毒性
基金项目(Foundation): 国家自然科学基金(No.20777055);; 高等学校博士学科点专项科研基金(No.20090072120058)
作者(Author): 徐挺;赵静;胡霞林;尹大强;
Email:
DOI:
参考文献(References):
- Bernard B K,Hoberman A M,Brown WR,et al.2002.Oral(ga-vage)two-generation(one litter per generation)reproduction study ofpentachlorophenol(penta)in rats[J].International Journal of Toxi-cology,21(4):301-318
- Bodine P V N.2008.Wnt signaling control of bone cell apoptosis[J].Cell Research,18(2):248-253
- Bolouri H,Davidson E H.2002.Modeling transcriptional regulatorynetworks[J].Bioessays,24(12):1118-1129
- Brazma A,Krestyaninova M,Sarkans U.2006.Standards for sys-tems biology[J].Nature Reviews Genetics,7(8):593-605
- Bundy J G,Sidhu J K,Rana F,et al.2008.Systems toxicology'ap-proachidentifies coordinated metabolic responses to copperin a terres-trial non-model invertebrate,the earthworm Lumbricus rubellus[J].Bmc Biology,6:25
- Chan T M,Longabaugh W,Bolouri H,et al.2009.Developmentalgene regulatory networks in the zebrafish embryo[J].Biochi mica EtBiophysica Acta-Gene Regulatory Mechanisms,1789(4):279-298
- Cho H,Ki m S J,Park H W,et al.2010.Arelationship betweenmiRNAand gene expressionin the mouse sertoli cell line after expo-sure to bisphenol A[J].Biochip Journal,4(1):75-81
- Cooper GS,Jones S.2008.Pentachlorophenol andcancer risk:Focu-singthelens onspecific chlorophenols and contaminants[J].Environ-mental Health Perspectives,116(8):1001-1008
- Coumoul X,Deng C X.2003.Roles of FGFreceptors in mammaliandevelopment and congenital diseases[J].Birth Defects Research(PartC),69(4):286-304
- Craig A,Sidaway J,Hol mes E,et al.2006.Systems toxicology:In-tegrated genomic,proteomic and metabonomic analysis of metha-pyrileneinduced hepatotoxicityinthe rat[J].Journal of Proteome Re-search,5(7):1586-1601
- Cummings A,Kavlock R.2005.Asystems biology approach to de-velopmental toxicology[J].Reproductive Toxicology,19(3):281-290
- Davidson E H.2006.The Regulatory Genome:Gene Regulatory Net-works in Development and Evolution[M].New York,AcademicPress
- Davidson E H,Erwin D H.2006.Gene regulatory networks and theevolution of ani mal body plans[J].Science,311(5762):796-800
- Davidsona E H,Levine MS.2008.Properties of developmental generegulatory networks[J].Proceedings of the National Academy of Sci-ences of the United States of America,105(51):20063-20066
- Davidson E H,Rast J P,Oliveri P,et al.2002.Agenomic regulato-ry networkfor development[J].Science,295(5560):1669-1678
- De-Leon S B,Davidson E H.2009.Experi mentally based sea urchingene regulatory network and the causal explanation of developmentalphenomenology[J].Systems Biology and Medicine,1(2):237-246
- Deng L,Hu S,Baydoun A R,et al.2009.Aspirininduces apoptosisin mesenchymal stemcells requiring Wnt/beta-catenin pathway[J].Cell Proliferation,42(6):721-730
- Duan Z H,Zhu L,Zhu L Y,et al.2008.Individual andjoint toxiceffects of pentachlorophenol and bisphenol A on the development ofzebrafish(Daniorerio)embryo[J].Ecotoxicology and Environmen-tal Safety,71(3):774-780
- Eivers E,Demagny H,De Robertis E M.2009.Integration of BMPand Wnt signaling via vertebrate Smad1/5/8and Drosophila Mad[J].Cytokine&Growth Factor Reviews,20(5-6):357-365
- Ellinger-Ziegelbauer H,Aubrecht J,Kleinjans J C,et al.2009.Ap-plication of toxicogenomics to study mechanisms of genotoxicity andcarcinogenicity[J].Toxicology Letters,186(1):36-44
- Erwin D H,Davidson E H.2009.The evolution of hierarchical generegulatory networks[J].Nature Reviews Genetics,10:141-148
- Ettensohn C A,Kitazawa C,Cheers MS,et al.2007.Gene regula-tory networks and developmental plasticityinthe early sea urchin em-bryo:Alternative deployment of the skeletogenic gene regulatory net-work[J].Development,134:3077-3087
- Ghosh P,Banerjee M,Giri A K,et al.2008.Toxicogenomics of ar-senic:Classical ideas and recent advances[J].Mutation Research-Re-views in Mutation Research,659(3):293-301
- Gohlke J M,Armant O,ParhamF M,et al.2008.Characterizationof the proneural gene regulatory network during mouse telencephalondevelopment[J].Bmc Biology,6:15
- Itoh N.2007.The Fgf familiesin humans,mice,andzebrafish:Theirevolutional processes and roles in development,metabolism,and dis-ease[J].Biological&Pharmaceutical Bulletin,30(10):1819-1825
- James D,Levine AJ,Besser D,et al.2005.TGFbeta/activin/nodalsignalingis necessary for the maintenance of pluripotency in humanembryonic stemcells[J].Development,132(6):1273-1282
- Johnston RJ Jr,Chang S,Etchberger J F,et al.2005.MicroRNAsacting ina double-negativefeedbackloopto control a neuronal cell fatedecision[J].Proceedings of the National Academy of Sciences of theUnited States of America,102(35):12449-12454
- Kato H,Furuhashi T,Tanaka M,et al.2006.Effects of bisphenolAgiven neonatally on reproductive functions of male rats[J].Repro-ductive Toxicology,22(1):20-29
- Kawakami Y,Capdevila J,Buscher D,et al.2001.Wnt signals con-trol FGF-dependent li mbinitiationand AERinductioninthe chickem-bryo[J].Cell,104(6):891-900
- Keshishian H,Ki m YS.2004.Orchestrating development and func-tion:Retrograde BMPsignalinginthe Drosophila nervous system[J].Trends in Neurosciences,27(3):143-147
- Klaassen C D.2008.Casarett and Doull's Toxicology:The Basic Sci-ence of Poisons[M].New York:McGraw-Hill
- Kohn A D,Moon R T.2005.Wnt and calciumsignaling:beta-Cate-nin-independent pathways[J].Cell Calcium,38(3-4):439-446
- Levine M,Davidson E H.2005.Gene regulatory networks for devel-opment[J].Proceedings of the National Academy of Sciences of theUnited States of America,102(14):4936-4942
- Longabaugh WJ R,Davidson E H,Bolouri H.2005.Computationalrepresentation of developmental genetic regulatory networks[J].De-velopmental Biology,283(1):1-16
- Maes OC,An J,Sarojini H,et al.2008.Changesin microRNAex-pression patterns in human fibroblasts after low-LET radiation[J].Journal of Cellular Biochemistry,105(3):824-834
- Maffini M V,Rubin B S,Sonnenschein C,et al.2006.Endocrinedisruptors and reproductive health:The case of bisphenol-A[J].Mo-lecular and Cellular Endocrinology,254:179-186
- Materna S C,Oliveri P.2008.Aprotocol for unraveling gene regula-tory networks[J].Nature Protocols,3(12):1876-1887
- Mattingly CJ,Hampton T H,Brothers K M,et al.2009.Perturba-tion of defense pathways bylow-dose arsenic exposureinzebrafishem-bryos[J].Environmental Health Perspectives,117(6):981-987
- Moens L N,Smolders R,Van der Ven K,et al.2007.Effluent i m-pact assessment using micro array-based analysis in common carp:Asystems toxicology approach[J].Chemosphere,67(11):2293-2304
- Morley R H,Lachani K,Keefe D,et al.2009.A gene regulatorynetwork directed by zebrafish No tail accounts for its roles in meso-dermformation[J].Proceedings of the National Academy of Sciencesof the United States of America,106(10):3829-3834
- Oliveri P,Carrick D M,Davidson E H.2002.Aregulatory gene net-work that directs micromere specification in the sea urchin embryo[J].Developmental Biology,246(1):209-228
- Owens K D,Baer K N.2000.Modifications of the topical Japanesemedaka(Oryzias latipes)embryolarval assay for assessing develop-mental toxicity of pentachlorophenol and p,p'-dichlorodiphenyltrichlo-roethane[J].Ecotoxicology and Environmental Safety,47(1):87-95
- Pillai MC,Vines C A,Wikramanayake A H,et al.2003.Polycyclicaromatic hydrocarbons disrupt axial developmentinsea urchinembryosthrough a beta-catenin dependent pathway[J].Toxicology,186(1-2):93-108
- Revilla-i-Domingo R,Davidson E H.2003.Developmental gene network analysis[J].International Journal of Developmental Biology,4(7-8):695-703
- Ruden D M,Chen L,Possidente D,et al.2009.Genetical toxicog-enomics in Drosophila identifies master-modulatory loci that are regu-lated by developmental exposure tolead[J].Neurotoxicology,30(6):898-914
- Sekizawa J.2008.Low-dose effects of bisphenol A:Aserious threatto human health[J].Journal of Toxicological Sciences,33(4):389-403
- Shen M M.2007.Nodal signaling:Developmental roles and regula-tion[J].Development,134:1023-1034
- Smith J.2008.A protocol describing the principles of cis-regulatoryanalysis inthe sea urchin[J].Nature Protocols,3:710-718
- Smith J,Davidson E H.2008.Gene regulatory network subcircuitcontrolling a dynamic spatial pattern of signalinginthe sea urchin em-bryo[J].Proceedings of the National Academy of Sciences of the U-nited States of America,105(51):20089-20094
- Solnica-Krezel L,Kelly G.2009.Thenand nowof zebrafish Wnt sig-naling[J].Zebrafish,6(1):1
- Tada M,Kai M.2009.Noncanonical Wnt/PCPsignaling during ver-tebrate gastrulation[J].Zebrafish,6(1):29-40
- Tennant R W.2002.The national center for toxicogenomics:Usingnewtechnologies toinform mechanistic toxicology[J].EnvironmentalHealth Perspectives,110(1):A8-A10
- Vallier L,Alexander M,Pedersen R A.2005.Activin/Nodal andFGF pathways cooperateto maintain pluripotency of humanembryonicstemcells[J].Journal of Cell Science,118:4495-4509
- Varga M,Young R,Wilson S.2009.Canonical Wnt signallinginthedevelopment of the zebrafish optic tecturn[J].Mechanisms of Devel-opment,126:S278-S278
- Vokes S A,Ji H K,McCuine S,et al.2007.Genomic characteriza-tion of Gli-activator targetsinsonic hedgehog-mediated neural pattern-ing[J].Development,134(10):1977-1989
- VomSaal FS,Hughes C.2005.Anextensive newliterature concern-inglow-dose effects of bisphenol Ashows the needfor a newrisk as-sessment[J].Environmental Health Perspectives,113(8):926-933
- Wada H,Okamoto H.2009.Roles of noncanonical Wnt/PCP path-way genes in neuronal migration and neurulationin zebrafish[J].Ze-brafish,6(1):3-8
- Waters M,Boorman G,Bushel P,et al.2003.Systems toxicologyand the chemical effects in biological systems(CEBS)knowledge base[J].Environmental Health Perspectives,111(6):811-824
- Waters MD,Fostel J M.2004.Toxicogenomics and systems toxicol-ogy:Ai ms and prospects[J].Nature Reviews Genetics,5:936-948
- Weitzel HE,Illies MR,ByrumC A,et al.2004.Differential sta-bility of beta-catenin along the ani mal-vegetal axis of the sea urchinembryo mediated by disheveled[J].Development,131(12):2947-2956
- Welshons W V,Thayer K A,Judy B M,et al.2003.Largeeffects fromsmall exposures.I.Mechanisms for endocrine-dis-rupting chemicals with estrogenic activity[J].EnvironmentalHealth Perspectives,111(8):994-1006
- Wu Z Y,Hu P,Zhao Q S,et al.2009a.Exploration of devel-opmental toxicity mechanism of pentachlorophenol using cDNAmicroarray[J].Chinese Journal of Environmental Science,30(11):3382-3387(in Chinese)
- Wu Z Y,Hu P,Zhao Q S,et al.2009b.Effects of pentachlo-rophenol on the Wnt signaling during the development of ze-brafish embryo[J].Asian Journal of Ecotoxicology,4(4):494-499(in Chinese)
- Yin Y,White A C,Huh S H,et al.2008.An FGF-WNTgeneregulatory network controls lung mesenchyme development[J].Developmental Biology,319(2):426-436
- Zhu H K,Wu Z Y,Zhao QS,et al.2008.Expression changesof apoptosis related genes after pentachlorophenol exposure andmolecular cloning and phylogenetic analysis of caspase-2in ze-brafish[J].Asian Journal of Ecotoxicology,3(4):356-362(in Chinese)
- 吴兆毅,胡平,赵庆顺,等.2009a.利用基因芯片探讨五氯酚发育毒性的作用机制[J].环境科学,30(11):3382-3387
- 吴兆毅,胡平,赵庆顺,等.2009b.五氯酚对斑马鱼胚胎发育期Wnt信号通路的影响[J].生态毒理学报,4(4):494-499
- 朱含开,吴兆毅,赵庆顺,等.2008.五氯酚暴露诱导斑马鱼胚胎细胞凋亡相关基因的变化及caspase-2基因克隆和系统进化分析[J].生态毒理学报,3(4):356-362