人GJB2分子进化与耳聋遗传效应的关联性分析

间隙连接蛋白β2(GJB2)基因突变与遗传性非综合征性耳聋密切相关,其广泛的突变类型及特异性的热点突变被认为是一种独特的致聋基因。本研究应用生物信息学方法对17个物种的GJB2蛋白进行了系统发育、保守性、跨膜区结构、三维结构和错义突变的分析,并结合已有报道的实验结果进行关联性分析。分析预测获得了166个固定的氨基酸位点、2个非保守区以及2个空间结构保守位点;关联性分析证实发生在保守位点的突变致病性高,非保守区突变的概率致病性小,跨膜区且改变氨基酸性质的突变,可能影响蛋白的空间结构而改变膜通道的通透性。本文为进一步研究GJB2基因突变与聋病的关联性及分子发病机制提供了理论依据,同时,这种研究思路对其它疾病的相关研究具有一定的借鉴价值。     

眼皮肤白化病患者酪氨酸酶基因突变的研究

目的：对临床诊断为眼皮肤白化病（OCA）患者的酪氨酸酶（TYR）基因进行突变筛查,了解我国大陆OCA患者TYR基因突变类型,探讨基因突变对人TYR蛋白结构和功能的影响。方法：应用PCR技术,扩增患者及其父母的TYR基因外显子、外显子-内含子交界区及启动子区;以DNA序列测定技术,进行突变筛查与鉴定;利用生物信息学方法,对突变引起蛋白结构和功能的改变进行预测与分析。结果：在15名患者的30个TYR等位基因内,查明11种突变;其中错义突变5种（W400L、R299H、E294K、R77Q和K142M）,无义突变3种（R116X、R278X和G295X）,插入突变2种（929insC和232insGGG）,剪切位点突变1种（IVS1-3 C〉G）;对4个突变W400L、R299H、929insC、232insGGG的生物信息学分析显示,突变的致病性与蛋白结构和功能的改变相关。结论：W400L占本研究所检出全部OCA1突变等位基因的30．0％（9／30）,可能为中国大陆人群中较常见的TYR基因突变类型;应用生物信息学分析方法对TYR基因突变的致病性做出一些合理可能的解释是可行的。     

小鼠Agouti基因变异及生物信息学分析

目的分析候选基因Agouti的多态性,揭示染色体工程小鼠毛色差异的分子机制。方法首先,用测色仪检测小鼠的毛色差异。其次,利用DNA芯片进行全基因组扫描确定候选基因Agouti。最后,运用生物信息学软件分析Agouti基因cDNA序列和氨基酸序列的多态性,预测突变对蛋白结构和功能产生的影响。结果发现Agouti基因cDNA序列上存在5个SNPs,使Agouti信号蛋白产生了3个错义突变。生物信息学分析发现,其中一个错义突变使该蛋白丢失了一个β折叠,并且其三级结构发生改变,最终导致与受体结合的能力相较于野生型有所下降。结论在毛色基因Agouti的编码区发现了一个新的错义突变,该突变使Agouti信号蛋白与受体结合能力下降,最终导致小鼠的毛色由浅灰色变为深灰色。     

mtATPase6基因变异与弱精子症的相关分析

为了分析mtATPase6基因突变与弱精子症的相关性,按wHO标准收集了27例弱精子症精液标本和28例精子活力正常精液标本,PCR扩增mtATPase6基因,纯化测序,分析mtATPase6基因突变,比较两组突变频率的差异.结合生物信息学工具分析错义突变位点的氨基酸进化保守性及其蛋白质部分三级结构.结果显示:发现了6个未曾报道过的突变位点;弱精子症组mtATPase6基因平均突变率显著高于对照组,可能与弱精子症有一定的相关性.G8584A、A8701G和G9053A三个错义突变可能是多态性位点,其余8个错义突变中的6个具有进化保守性的位点累计突变频率显著高于对照组,这些位点突变可能与弱精子症有关.     

中国荷斯坦牛ABCG2基因编码区多态性检测及生物信息学分析

目的：研究中国荷斯坦牛ABCG2基因编码区（CDS）多态性,并进行生物信息学分析。方法：以中国荷斯坦牛为材料,利用PCR-SSCP技术对ABCG2基因CDS多态性进行检测,然后预测蛋白质序列的改变,并用生物信息学软件对蛋白质序列突变前后的结构及性质进行分析。结果：在外显子9中存在一个A→G碱基突变,导致氨基酸由酪氨酸突变为半胱氨酸,将此突变命名为Y367C;在外显子14中存在一个G→A突变,导致氨基酸由精氨酸突变为谷氨酰胺,将此突变命名为R578Q。2个突变一个位于功能区与跨膜区之间,一个位于跨膜区。生物信息学分析发现,蛋白质二级结构增加了1个卷曲（C）和2个转角（T）,同时减少了3个β折叠（E）,且ABCG2蛋白的组成和一些性质也发生了改变。结论：检测到的2个单核苷酸多态性引起了ABCG2蛋白性质和二级结构的改变;为进一步研究ABCG2蛋白对产乳性状的影响奠定了基础。     

江口萝卜猪FABPs主要家族基因SNPs筛选及生物信息学分析

以江口萝卜猪为试验材料构建DNA池,采用直接测序技术对猪L-FABP、I-FABP、H-FABP、A-FABP基因进行SNPs快速筛查,共检测出7个SNPs,分别为intron1-T1745C、exon2-T125C、exon2-A131C、exon2-C153A、exon2-A65T、exon2-G40A、intron3-C65T。其中intron1-T1745C、intron3-C65T位于内含子上;exon2-T125C、exon2-C153A为同义突变;exon2-A131C、exon2-A65T、exon2-G40A为错义突变,分别使编码氨基酸发生Glu→Ala、Lys→Met、Glu→Lys的改变,对其进行生物信息学分析表明,突变前后的等位基因频率估算,mR NA二级结构预测,蛋白质二级、三级结构预测分析均有差异。     

SGTA基因及其蛋白的生物信息学分析

[目的]对SGTA基因及其蛋白的结构和特征进行生物信息学分析,为研究SGTA与肿瘤形成和发展的相关性提供理论基础。[方法]运用生物信息学数据库和软件对SGTA基因的结构、单核苷酸多态性位点(SNP)、SGTA基因与其他基因的相互作用网络、SGTA蛋白的理化性质、二级结构、蛋白结构域、蛋白翻译后修饰、蛋白质之间相互作用网络进行分析。[结果]人SGTA基因有5种可变剪接产物,编码区存在78个SNP位点,其中错义突变31个,无义突变1个。人SGTA蛋白由313个氨基酸组成,是稳定性不高的亲水蛋白,α-螺旋是其主要二级结构元件,属于TRP超家族,预测有3个磷酸化激酶修饰位点和数个潜在泛素化修饰位点。与SGTA存在相互作用的基因和蛋白多数与维持体内蛋白质稳定的分子伴侣功能相关。[结论]SGTA基因及其蛋白的生物信息学分析为进一步实验研究其在肿瘤形成和发展中的地位及调控机制奠定了基础。     

BRCA1蛋白的序列及空间结构的分析

查询人的BRCA1蛋白的氨基酸序列,利用生物信息学的方法进行相似性搜索,获得一系列BRCA1蛋白的氨基酸序列。选择了其中的11条序列,对BRCA1蛋白进行了多重序列分析和进化分析,对BRCA1蛋白的BRCT结构域进行三维同源模型的构建与比较分析。分析结果表明:BRCA1中某些特定部位的氨基酸序列高度保守;确定氨基酸的保守位点并联合进化分析可对基因错义突变的致病性做初步地猜测;相近物种来源的BRCA1具有较近的亲缘关系,而且具有极其相似的三维空间结构。这些为研究BRCA1蛋白的结构与功能关系提供指导意义。     

位点致病性预测软件对错义突变的预测效用评估

通过比较不同位点致病性预测软件的预测效果和预测特点,从而根据错义突变所在疾病的类型和使用目的选择预测效果最佳的软件,为位点致病性预测软件的合理有效使用提供依据。将孟德尔疾病和复杂疾病作为数据集分类标准,使用经实验验证的致病错义突变数据集对7种位点致病性预测软件(Mutation Taster-2,Mutation Assessor,Poly Phen2,SIFT,LRT,Condel和Logit)的实际预测效果和特点进行比较分析。结果显示被测位点致病性预测软件的预测效用和特点各不相同,同时软件对于孟德尔疾病数据集的预测效果优于复杂疾病数据集;此外Condel和Logit软件作为组合型位点致病性预测软件,在孟德尔疾病和复杂疾病错义突变数据集中的预测效果均优于单一型位点致病性预测软件,但二者的敏感度和特异性差异也较大。在位点致病性预测软件的实际使用过程中,应根据错义突变所属疾病的类型和软件的特点选择最适软件,或同时使用多个预测特点互补的软件对位点的致病性进行综合预测。     

宗地花猪和从江香猪ADRP基因多态性及生物信息学分析

为研究宗地花猪和从江香猪ADRP基因的单核苷酸多态性,为选种选育提供理论参考,试验以宗地花猪和从江香猪为对象,构建DNA池,采用PCR产物测序法对ADRP基因8个外显子进行单核苷酸多态性检测,并利用生物信息学方法对ADRP基因编码产物进行结构功能预测。结果显示,在两个猪种ADRP基因中筛查到5个SNPs,分别是T37C、T140C、G777A、A1061G、A1117G,其中T37C位于非编码区内,T140C和A1061G为同义突变,G777A(Val→Ile)和A1117G(Asn→Ser)为错义突变;突变前后ADRP基因m RNA二级结构、编码蛋白二级结构及三级结构均发生了变化。研究结果表明,宗地花猪和从江香猪ADRP基因具有较高的遗传多样性,可为猪种的选育和创新提供参考。     

Evaluation of the pathogenicity of GJB3 and GJB6 variants associated with nonsyndromic hearing loss

A number of genes responsible for hearing loss are related to ion recycling and homeostasis in the inner ear. Connexins (Cx26 encoded by GJB2, Cx31 encoded by GJB3 and Cx30 encoded by GJB6) are core components of gap junctions in the inner ear. Gap junctions are intercellular communication channels and important factors that are associated with hearing loss. To date, a molecular genetics study of GJB3 and GJB6 as a causative gene for hearing loss has not been performed in Korea. This study was therefore performed to elucidate the genetic characteristics of Korean patients with nonsyndromic sensorineural hearing loss and to determine the pathological mechanism of hearing loss by analyzing the intercellular communication function of Cx30 and Cx31 variants. Sequencing analysis of the GJB3 and GJB6 genes in our population revealed a total of nine variants, including four novel variants in the two genes. Three of the novel variants (Cx31-p.V27M, Cx31-p.V43M and Cx-30-p.I248V) and two previously reported variants (Cx31-p.V84I and Cx30-p.A40V) were selected for functional studies using a pathogenicity prediction program and assessed for whether the mutations were located in a conserved region of the protein. The results of biochemical and ionic coupling tests showed that both the Cx31-p.V27M and Cx31-p.V84I variants did not function normally when each was expressed as a heterozygote with the wild-type Cx31. This study demonstrated that two variants of Cx31 were pathogenic mutations with deleterious effect. This information will be valuable in understanding the pathogenic role of GJB3 and GJB6 mutations associated with hearing loss.     

Hearing loss: frequency and functional studies of the most common connexin26 alleles

Mutations in the GJB2 gene, encoding the gap-junction channel protein connexin 26, account for the majority of recessive forms and some of the dominant cases of deafness. Here, we report the frequency of GJB2 alleles in the Italian population affected by hearing loss and the functional analysis of six missense mutations. Genetic studies indicate that, apart from the common 35delG, only few additional mutations can be detected with a significant frequency in our population. Transfection of communication-incompetent HeLa cells with Cx26 missense mutations revealed three distinct classes of functional deficits in terms of protein expression, subcellular localisation and/or functional activity. Moreover, the M34T mutant acted as a dominant inhibitor of wild-type Cx26 channel activity when the two proteins were co-expressed in a manner mimicking a heterozygous genotype. These data support the hypothesis of a functional role for M34T as a dominant allele and represent a further step towards a complete understanding of the role of GJB2 in causing hearing loss.     

The spectrum of mutations in erythrokeratodermias – novel and de novo mutations in GJB3

Intercellular channels in skin are a complex and functionally diverse system formed by at least eight connexins (Cx). Our recent molecular studies implicating Cx defects in inherited skin disorders emphasize the critical role of this signaling pathway in epidermal differentiation. Erythrokeratodermia variabilis (EKV) is an autosomal dominant genodermatosis with a striking phenotype characterized by the independent occurrence of transient localized erythema and hyperkeratosis. The disease maps to 1p34-p35, and recently we identified the causative gene GJB3 encoding Cx31. We have now investigated GJB3 in two families and three sporadic cases with EKV, and report three new heterozygous mutations. In a sporadic case, we detected a mutation leading to substitution of a conserved phenylalanine (F137L) in the third transmembrane domain, which likely interferes with the proper assembly or gating properties of connexons. In another family, all three affected individuals carried two distinct mutations on the same GJB3 allele. However, only a de novo heterozygous missense mutation replacing arginine 42 with proline (R42P) co-segregated with the disease, while a 12 bp deletion predicted to eliminate four amino acid residues in the variable carboxy terminal domain of Cx31 was also found in clinically unaffected relatives but not in 90 unaffected controls. Including the previously published mutations, in toto, five different missense mutations have now been detected in 6 out of 17 families investigated by our laboratory, all of which presumably affect the cytoplasmic amino terminal and transmembrane domains of Cx31. In contrast, two mutations linked to progressive high-tone hearing impairment were located in the second extracellular domain, suggesting that the character and position of Cx mutations determine their phenotypic expression in different tissues. However, the phenotypic spectrum of GJB3 mutations seems not to include progressive symmetric erythrokeratodermia, another dominant genodermatosis with overlapping features, since no mutations were found in six unrelated families tested.     

Digenic inheritance of non-syndromic deafness caused by mutations at the gap junction proteins Cx26 and Cx31

Mutations in the genes coding for connexin 26 (Cx26) and connexin 31 (Cx31) cause non-syndromic deafness. Here, we provide evidence that mutations at these two connexin genes can interact to cause hearing loss in digenic heterozygotes in humans. We have screened 108 GJB2 heterozygous Chinese patients for mutations in GJB3 by sequencing. We have excluded the possibility that mutations in exon 1 of GJB2 and the deletion of GJB6 are the second mutant allele in these Chinese heterozygous probands. Two different GJB3 mutations (N166S and A194T) occurring in compound heterozygosity with the 235delC and 299delAT of GJB2 were identified in three unrelated families (235delC/N166S, 235delC/A194T and 299delAT/A194T). Neither of these mutations in Cx31 was detected in DNA from 200 unrelated Chinese controls. Direct physical interaction of Cx26 with Cx31 is supported by data showing that Cx26 and Cx31 have overlapping expression patterns in the cochlea. In addition, by coimmunoprecipitation of mouse cochlear membrane proteins, we identified the presence of heteromeric Cx26/Cx31 connexons. Furthermore, by cotransfection of mCherry-tagged Cx26 and GFP-tagged Cx31 in human embryonic kidney (HEK)-293 cells, we demonstrated that the two connexins were able to co-assemble in vitro in the same junction plaque. Together, our data indicate that a genetic interaction between these two connexin genes can lead to hearing loss.     

Screening for mutations in the GJB3 gene in Brazilian patients with nonsyndromic deafness

Deafness is a complex disorder that is affected by a high number of genes and environmental factors. Recently, enormous progress has been made in nonsyndromic deafness research, with the identification of 90 loci and 33 nuclear and 2 mitochondrial genes involved (http://dnalab-www.uia.ac.be/dnalab/hhh/). Mutations in the GJB3 gene, encoding the gap junction protein connexin 31 (Cx31), have been pathogenically linked to erythrokeratodermia variabilis and nonsyndromic autosomal recessive or dominant hereditary hearing impairment. To determine the contribution of the GJB3 gene to sporadic deafness, we analysed the GJB3 gene in 67 families with nonsyndromic hearing impairment. A single coding exon of the GJB3 gene was amplified from genomic DNA and then sequenced. Here we report on three amino acid changes: Y177D (c.529T > G), 49delK (c.1227C > T), and R32W (c.144-146delGAA). The latter substitution has been previously described, but its involvement in hearing impairment remains uncertain. We hypothesize that mutations in the GJB3 gene are an infrequent cause of nonsyndromic deafness.     

Functional defects of Cx26 resulting from a heterozygous missense mutation in a family with dominant deaf-mutism and palmoplantar keratoderma

Mutations in GJB2 encoding the gap junction protein connexin-26 (Cx26) have been established as the basis of autosomal recessive non-syndromic hearing loss. The involvement of GJB2 in autosomal dominant deafness has also been proposed, although the putative mutation identified in one family with both deafness and palmoplantar keratoderma has recently been suggested to be merely a non-disease associated polymorphism. We have observed a similar phenotype in an Egyptian family that segregated with a heterozygous missense mutation of GJB2, leading to a non-conservative amino acid substitution (R75W). The deleterious dominant-negative effect of R75W on gap channel function was subsequently demonstrated in the paired oocyte expression system. Not only was R75W alone incapable of inducing electrical conductance between adjacent cells, but it almost completely suppressed the activity of co-expressed wildtype protein. The Cx26 mutant W77R, which has been implicated in autosomal recessive deafness, also failed to form functional gap channels by itself but did not significantly interfere with the function of wildtype Cx26. These data provide compelling evidence for the serious functional consequences of Cx26 mutations in dominant and recessive deafness. Received: 22 June 1998 / Accepted: 15 July 1998     

Functional studies of human skin disease- and deafness-associated connexin 30 mutations

Connexin 30 (Cx30) is a component of the gap junction complex. Dominant and recessive mutations in the GJB6 gene encoding Cx30 are associated with a variety of human inherited diseases primarily affecting the epidermis, hair, nail, and/or the inner ear. The underlying mechanism of disease associated with different GJB6 mutations such as the disruption of gap junction mediated intercellular communication is unknown. Towards understanding these disease mechanisms, transfection studies were performed in a keratinocyte cell line and in HeLa cells using EGFP tagged wildtype Cx30 and mutant Cx30 constructs harbouring dominant disease-associated GJB6 mutations. For all three of the skin disease-associated Cx30 mutations investigated, impaired trafficking of the protein to the plasma membrane was observed thus preventing the formation of functional Cx30 gap junctions. In contrast, the deafness-associated mutation T5M-Cx30/EGFP trafficked to the membrane but defective channel activity was observed following dye transfer studies.     

Functional characterization of a novel Cx26 (T55N) mutation associated to non-syndromic hearing loss

Mutations of the GJB2 gene, encoding connexin 26, are the most common cause of hereditary congenital hearing loss in many countries and account for up to 50% of cases of autosomal-recessive non-syndromic deafness. By contrast, only a few GJB2 mutations have been reported to cause an autosomal-dominant form of non-syndromic deafness. Here, we report a family from Southern Italy affected by non-syndromic autosomal dominant post-lingual hearing loss, due to a novel missense mutation in the GJB2 gene, a threonine to asparagine amino acid substitution at codon 55 (T55N). Functional studies indicated that the mutation T55N produces a protein that, although expressed to levels similar to those of the wt counterpart, is deeply impaired in its intracellular trafficking and fails to reach the plasma membrane. The mutation T55N is located at the apex of the first extracellular loop of the protein, a region suggested to play a role in protein targeting and a site for other two mutations, G59A and D66H, causing dominant forms of deafness.     

Connexin mutations in hearing loss,dermatological and neurological disorders

Gap junctions are important structures in cell-to-cell communication. Connexins, the protein units of gap junctions, are involved in several human disorders. Mutations in beta-connexin genes cause hearing, dermatological and peripheral nerve disorders. Recessive mutations in the gene encoding connexin 26 (GJB2) are the most common cause of childhood-onset deafness. The combination of mutations in the GJB2 and GJB6 (Cx30) genes also cause childhood hearing impairment. Although both recessive and dominant connexin mutants are functionally impaired, dominant mutations might have in addition a dominant-negative effect on wild-type connexins. Some dominant mutations in beta-connexin genes have a pleiotropic effect at the level of the skin, the auditory system and the peripheral nerves. Understanding the genotype-phenotype correlations in diseases caused by mutations in connexin genes might provide important insight into the mechanisms that lead to these disorders.