先天性白内障相关基因热休克转录因子4非同义单核苷酸多态性高危致病表型的预测研究
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摘要
目的系统整合、收集单核苷酸多态性数据库和文献中热休克转录因子4(HSF4)基因非同义单核苷酸多态性(nsSNP)的信息,筛选具有高危致病的nsSNP位点。方法从单核苷酸多态性数据库、临床变异数据库、人类基因突变数据库、疾病基因网络数据库和已发表文献中,收集整理HSF4基因的nsSNP数据。利用6款突变预测软件,进行致病性预测分析,筛选高危致病nsSNP位点。应用I-变异2.0在线软件、突变所致蛋白质稳定性改变预测软件和非同义突变对蛋白质稳定性的影响软件比较氨基酸替换对蛋白质稳定性的影响,利用氨基酸保守性评估在线软件、带对齐的自优化预测在线软件和蛋白释意软件对nsSNP位点中氨基酸进化保守性、理化性质和突变前后的蛋白结构改变进行预测分析。结果通过以上数据库检索以及基因突变致病性预测软件分析,共获得31个HSF4b(HSF4基因选择性剪切形成的一种亚型)高危致病nsSNP位点。其中,11个nsSNP位点已在文献中报道,并指出与先天性白内障相关;20个nsSNP位点为本研究预测的高危致病性位点。高危致病nsSNP位点可导致25个野生型氨基酸位点被31个突变型氨基酸替换,替换的突变型氨基酸中预测有25个可能导致蛋白质稳定性下降。除了39位色氨酸外,其余24个野生型氨基酸均为高度进化保守性位点。20个位于热休克转录因子脱氧核糖核酸结合域,5个位于疏水重复序列,而成为高危致病nsSNP位点。本研究预测发现这些高危致病性位点氨基酸突变后均可导致氨基酸和蛋白质的理化性质改变,导致蛋白质二级和三级结构改变、结构域与其他分子之间相互作用的改变,进而影响蛋白功能。结论本研究预测筛选获得的31个HSF4b基因高危致病nsSNP位点,其中20个为首次报道。推测这些高危致病nsSNP位点可能是参与先天性白内障发病的重要位点,将为临床及理论研究提供重要的参考基础。
Objective The aim of this study was to systematically integrate and collect non-synonymous single nucleotide polymorphism(nsSNP) information of heat shock transcription factor 4(HSF4) gene in single nucleotide polymorphism database and literature, and screen nsSNP loci with high risk of pathogenicity. Methods The nsSNP data of HSF4 gene were collected from dbSNP database, ClinVar database, HGMD database, DisGeNET database and published literature. The pathogenicity was predicted and analyzed by 6 software tools including Mutpred2, PANTHER-PSEP, PhD-SNP, PolyPhen 2.0, PROVEAN and SIFT. The high-risk pathogenic nsSNP was screened. I-Mutant 2.0, MUpro and INPS online software tools were used to compare the effects of amino acid substitution on protein stability. ConSurf, The Self-Optimized Prediction Method With Alignment(SOPMA) and Have(y)Our Protein Explained(HOPE) online software tools were used to predict the conservativeness of amino acid evolution, physicochemical properties and changes of protein structure before and after mutation. Results 31 HSF4b high-risk pathogenic nsS NPs were obtained by searching the mentioned databases and analyzing the results of genetic mutation pathogenicity prediction software tools. Among them,11 nsS NPs were reported to be associated with congenital cataract and 20 were newly predicted high-risk pathogenic nsS NPs. High-risk pathogenic nsS NPs could cause 25 wild-type amino acids to be replaced by 31 mutant amino acids,and 25 mutant amino acids could be predicted to lead to decline the stability of protein. The other 24 wild-type amino acids were highly evolutionary conservative sites except 39 tryptophan. Twenty sites were located in the heat shock transcription factor DNA binding domain and five in the hydrophobic repeat sequence HR-A/B and became high-risk pathogenic nsS NPs. It is predicted that the mutation of amino acids in these high-risk pathogenic sites could cause changes in the physical and chemical properties of amino acids and proteins,resulting in changes in secondary and tertiary structures of proteins and interaction effects between domains and other molecules,and thus affecting the function of proteins. Conclusions 31 high-risk pathogenic nsS NPs of HSF4 gene were predicted and screened in this study. Among of them,20 high-risk pathogenic nsS NPs were reported for the first time. These high-risk pathogenic nsS NPs might be important involved in the pathogenesis of congenital cataract and provide an important reference for clinical trials and theory studies.
Objective The aim of this study was to systematically integrate and collect non-synonymous single nucleotide polymorphism(nsSNP) information of heat shock transcription factor 4(HSF4) gene in single nucleotide polymorphism database and literature, and screen nsSNP loci with high risk of pathogenicity. Methods The nsSNP data of HSF4 gene were collected from dbSNP database, ClinVar database, HGMD database, DisGeNET database and published literature. The pathogenicity was predicted and analyzed by 6 software tools including Mutpred2, PANTHER-PSEP, PhD-SNP, PolyPhen 2.0, PROVEAN and SIFT. The high-risk pathogenic nsSNP was screened. I-Mutant 2.0, MUpro and INPS online software tools were used to compare the effects of amino acid substitution on protein stability. ConSurf, The Self-Optimized Prediction Method With Alignment(SOPMA) and Have(y)Our Protein Explained(HOPE) online software tools were used to predict the conservativeness of amino acid evolution, physicochemical properties and changes of protein structure before and after mutation. Results 31 HSF4b high-risk pathogenic nsS NPs were obtained by searching the mentioned databases and analyzing the results of genetic mutation pathogenicity prediction software tools. Among them,11 nsS NPs were reported to be associated with congenital cataract and 20 were newly predicted high-risk pathogenic nsS NPs. High-risk pathogenic nsS NPs could cause 25 wild-type amino acids to be replaced by 31 mutant amino acids,and 25 mutant amino acids could be predicted to lead to decline the stability of protein. The other 24 wild-type amino acids were highly evolutionary conservative sites except 39 tryptophan. Twenty sites were located in the heat shock transcription factor DNA binding domain and five in the hydrophobic repeat sequence HR-A/B and became high-risk pathogenic nsS NPs. It is predicted that the mutation of amino acids in these high-risk pathogenic sites could cause changes in the physical and chemical properties of amino acids and proteins,resulting in changes in secondary and tertiary structures of proteins and interaction effects between domains and other molecules,and thus affecting the function of proteins. Conclusions 31 high-risk pathogenic nsS NPs of HSF4 gene were predicted and screened in this study. Among of them,20 high-risk pathogenic nsS NPs were reported for the first time. These high-risk pathogenic nsS NPs might be important involved in the pathogenesis of congenital cataract and provide an important reference for clinical trials and theory studies.
引文
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[27] Yi J,Yun J,Li ZK,et al.Epidemiology and molecular genetics of congenital cataracts[J].Int J Ophthalmol,2011,4(4):422-432.
[28] Hamosh A,Scott AF,Amberger JS,et al.Online Mendelian Inheritance in Man (OMIM),a knowledgebase of human genes and genetic disorders[J].Nucleic Acids Res,2005,33:D514-D517.
[29] Bu L,Jin Y,Shi Y,et al.Mutant DNA-binding domain of HSF4 is associated with autosomal dominant lamellar and Marner cataract,Nat Genet,2002,31(3):276-278.
[30] Lv H,Huang C,Zhang J,et al.A novel HSF4 gene mutation causes autosomal-dominant cataracts in a Chinese family[J].Gene,2014,4(5):823-828.
[31] Gillespie RL,O′Sullivan J,Ashworth J,et al.Personalized diagnosis and management of congenital cataract by next-generation sequencing[J].Ophthalmology,2014,121(11):2124-2137.
[32] Li D,Wang S,Ye H,et al.Distribution of gene mutations in sporadic congenital cataract in a Han Chinese population[J].Mol Vis,2016,22:589-598.
[33] Cao Z,Zhu Y,Liu L,et al.Novel mutations in HSF4 cause congenital cataracts in Chinese families[J].BMC Med Genet,2018,19(1):150.
[34] Berry V,Pontikos N,Moore A,et al.A novel missense mutation in HSF4 causes autosomal-dominant congenital lamellar cataract in a British family[J].Eye,2018,32(4):806-812.
[35] Ke T,Wang QK,Ji B,et al.Novel HSF4 mutation causes congenital total white cataract in a Chinese family[J].Am J Ophthalmol,2006,142(2):298-303.
[36] Liu L,Zhang Q,Zhou LX,et al.A novel HSF4 mutation in a Chinese family with autosomal dominant congenital cataract[J].J Huazhong Univ Sci Technolog Med Sci,2015,35(2):316-318.
[37] Hansen L,Mikkelsen A,Nürnberg P,et al.Comprehensive mutational screening in a cohort of Danish families with hereditary congenital cataract[J].Invest Ophthalmol Vis Sci,2009,50(7):3291-3303.
[38] Behnam M,Imagawa E,Chaleshtori AR,et al.A novel homozygous mutation in HSF4 causing autosomal recessive congenital cataract[J].J Hum Genet,2016,61(2):177-179.
[39] Forshew T,Johnson CA,Khaliq S,et al.Locus heterogeneity in autosomal recessive congenital cataracts:linkage to 9q and germline HSF4 mutations[J].Hum Genet,2005,117(5):452-459.
[40] Khan S,M Vihinen.Performance of protein stability predictors[J].Hum Mutat,2010,31(6):675-684.
[41] 马汝海,钟连声,王天骄,等.转录因子HSF4的生物信息学分析[J].生命科学研究,2016,20(6):475-479.
[2] Tanabe M,Sasai N,Nagata K,et al.The mammalian HSF4 gene generates both an activator and a repressor of heat shock genes by alternative splicing[J].J Biol Chem,1999,274(39):27845-27856.
[3] Min JN,Zhang Y,Moskophidis D,et al.Unique contribution of heat shock transcription factor 4 in ocular lens development and fiber cell differentiation[J].Genesis,2004,40(4):205-217.
[4] Enoki Y,Mukoda Y,Furutani C,et al.DNA-binding and transcriptional activities of human HSF4 containing mutations that associate with congenital and age-related cataracts[J].Biochim Biophys Acta,2010,1802(9):749-753.
[5] Sheeladevi S,Lawrenson JG,Fielder AR,et al.Global prevalence of childhood cataract:a systematic review[J].Eye (Lond),2016,30(9):1160-1169.
[6] Shiels A ,Hejtmancik JF.Mutations and mechanisms in congenital and age-related cataracts[J].Exp Eye Res,2017,156:95-102.
[7] Pichi F,Lembo A,Serafino M,et al.Genetics of Congenital Cataract[J].Dev Ophthalmol,2016,57:1-14.
[8] Shiels A,Bennett TM,Hejtmancik JF.Cat-Map:putting cataract on the map[J].Mol Vis 2010,16:2007-2015.
[9] Collins FS,Brooks LD,Chakravarti A.A DNA polymorphism discovery resource for research on human genetic variation[J].Genome Res,1998,8(12):1229-1231.
[10] Sherry ST,Ward MH,Kholodov M,et al.dbSNP:the NCBI database of genetic variation[J].Nucleic Acids Res,2001,29(1):308-311.
[11] Landrum MJ,Lee JM,Benson M,et al.ClinVar:improving access to variant interpretations and supporting evidence[J].Nucleic Acids Res,2018,46(D1):D1062-D1067.
[12] Stenson PD,Mort M,Ball EV,et al.The Human Gene Mutation Database:towards a comprehensive repository of inherited mutation data for medical research,genetic diagnosis and next-generation sequencing studies[J].Hum Genet,2017,136(6):665-677.
[13] Pinero J,Bravo A,Queralt-Rosinach N,et al.DisGeNET:a comprehensive platform integrating information on human disease-associated genes and variants[J].Nucleic Acids Res,2017,45(D1):D833-D839.
[14] Pejaver V,Urresti J,Lugo-Martinez J,et al.MutPred2:inferring the molecular and phenotypic impact of amino acid variants [EB/OL].(2017-05-09)[ 2019-01-31].https://www.biorxiv.org/content/10.1101/134981v1.
[15] Tang H ,PD Thomas.PANTHER-PSEP:predicting disease-causing genetic variants using position-specific evolutionary preservation[J].Bioinformatics,2016,32(14):2230-2232.
[16] Capriotti E,Calabrese R,Casadio R.Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information[J].Bioinformatics,2006,22(22):2729-2734.
[17] Adzhubei IA,Schmidt S,Peshkin L,et al.A method and server for predicting damaging missense mutations[J].Nat Methods,2010,7(4):248-249.
[18] Choi Y,Chan AP .PROVEAN web server:a tool to predict the functional effect of amino acid substitutions and indels[J].Bioinformatics,2015,31(16):2745-2747.
[19] Sim NL,Kumar P,Hu J,et al.SIFT web server:predicting effects of amino acid substitutions on proteins[J].Nucleic Acids Res,2012,40:W452-W457.
[20] Capriotti E,Fariselli P,Casadio R.I-Mutant2.0:predicting stability changes upon mutation from the protein sequence or structure[J].Nucleic Acids Res,2005,33:W306-W310.
[21] Cheng J,Randall A,Baldi P.Prediction of protein stability changes for single-site mutations using support vector machines[J].Proteins,2006,62(4):1125-1132.
[22] Savojardo C,Fariselli P,Martelli PL,et al.INPS-MD:a web server to predict stability of protein variants from sequence and structure[J].Bioinformatics,2016,32(16):2542-2544.
[23] Ashkenazy H,Abadi S,Martz E,et al.ConSurf 2016:an improved methodology to estimate and visualize evolutionary conservation in macromolecules[J].Nucleic Acids Res,2016,44(W1):W344-W350.
[24] Geourjon C,G Deleage.SOPMA:significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments[J].Comput Appl Biosci,1995,11(6):681-684.
[25] Venselaar H,Te Beek TA,Kuipers RK,et al.Protein structure analysis of mutations causing inheritable diseases.An e-Science approach with life scientist friendly interfaces[J].BMC bioinformatics,2010,11(1):548.
[26] Gilbert C,Foster A.Childhood blindness in the context of VISION 2020——the right to sight[J].Bull World Health Organ,2001,79(3):227-232.
[27] Yi J,Yun J,Li ZK,et al.Epidemiology and molecular genetics of congenital cataracts[J].Int J Ophthalmol,2011,4(4):422-432.
[28] Hamosh A,Scott AF,Amberger JS,et al.Online Mendelian Inheritance in Man (OMIM),a knowledgebase of human genes and genetic disorders[J].Nucleic Acids Res,2005,33:D514-D517.
[29] Bu L,Jin Y,Shi Y,et al.Mutant DNA-binding domain of HSF4 is associated with autosomal dominant lamellar and Marner cataract,Nat Genet,2002,31(3):276-278.
[30] Lv H,Huang C,Zhang J,et al.A novel HSF4 gene mutation causes autosomal-dominant cataracts in a Chinese family[J].Gene,2014,4(5):823-828.
[31] Gillespie RL,O′Sullivan J,Ashworth J,et al.Personalized diagnosis and management of congenital cataract by next-generation sequencing[J].Ophthalmology,2014,121(11):2124-2137.
[32] Li D,Wang S,Ye H,et al.Distribution of gene mutations in sporadic congenital cataract in a Han Chinese population[J].Mol Vis,2016,22:589-598.
[33] Cao Z,Zhu Y,Liu L,et al.Novel mutations in HSF4 cause congenital cataracts in Chinese families[J].BMC Med Genet,2018,19(1):150.
[34] Berry V,Pontikos N,Moore A,et al.A novel missense mutation in HSF4 causes autosomal-dominant congenital lamellar cataract in a British family[J].Eye,2018,32(4):806-812.
[35] Ke T,Wang QK,Ji B,et al.Novel HSF4 mutation causes congenital total white cataract in a Chinese family[J].Am J Ophthalmol,2006,142(2):298-303.
[36] Liu L,Zhang Q,Zhou LX,et al.A novel HSF4 mutation in a Chinese family with autosomal dominant congenital cataract[J].J Huazhong Univ Sci Technolog Med Sci,2015,35(2):316-318.
[37] Hansen L,Mikkelsen A,Nürnberg P,et al.Comprehensive mutational screening in a cohort of Danish families with hereditary congenital cataract[J].Invest Ophthalmol Vis Sci,2009,50(7):3291-3303.
[38] Behnam M,Imagawa E,Chaleshtori AR,et al.A novel homozygous mutation in HSF4 causing autosomal recessive congenital cataract[J].J Hum Genet,2016,61(2):177-179.
[39] Forshew T,Johnson CA,Khaliq S,et al.Locus heterogeneity in autosomal recessive congenital cataracts:linkage to 9q and germline HSF4 mutations[J].Hum Genet,2005,117(5):452-459.
[40] Khan S,M Vihinen.Performance of protein stability predictors[J].Hum Mutat,2010,31(6):675-684.
[41] 马汝海,钟连声,王天骄,等.转录因子HSF4的生物信息学分析[J].生命科学研究,2016,20(6):475-479.