PCR-SSCP在检测Leber遗传性视神经病变线粒体DNA突变的应用

目的探讨PCR-SSCP技术检测Leber遗传性视神经病变(LHON)线粒体DNA(mtDNA)3个原发突变的最佳分析条件.方法应用PCR-SSCP技术检测LHON mtDNA,对主要影响SSCP分辨率的聚丙酰胺凝胶的浓度和组成优化分析,并与突变特异性引物PCR(MSP)、限制性片段长度多态性(FRLP)及测序结果相印证.结果 80g/L交联度为66:1的非变性聚丙酰胺凝胶能同时检出LHONmtDNA的三个原发致病突变,与MSP、FRLP及DNA测序的结果一致.结论该分析条件简便、快速,能有效地检测LHONmtDNA突变.     

家族性乳腺癌线粒体基因组控制区突变研究

目的研究家族性乳腺癌线粒体基因组控制区(D-loop区)突变的情况。方法用PCR技术,对来自21个家系的23例家族性乳腺癌患者和18名正常对照者线粒体DNA(mitochondrial DNA,mtDNA)的D-loop区进行扩增并基因测序,分析突变。结果在23例乳腺癌患者mtDNA的D-loop区共发现126个突变位点,4个为新发现的突变;37个突变分别发生在所有23例患者D-loop区的突变热点D310区;在所有突变中,第310位点的T→C,311～312位点的TC插入,522～523位点的CA缺失和527位点的C→G是高发突变位点;同一家系中乳腺癌患者D310区的突变与正常对照不同。结论家族性乳腺癌患者D310区的突变可能提高了其对乳腺癌的易感性。     

血友病A患者FⅧ基因联合诊断及其DNA测序突变分析

目的探讨血友病A(HA)患者及携带者的基因诊断方法及诊断率。方法对20例HA患者及家系成员采用长距离PCR扩增(LD-PCR)技术、限制性内切酶酶切位点连锁分析(BclⅠPCR/RFLP)、可变串联重复序列多态性分析(St14 VNTR/PCR);并对FⅧ基因18号内含子的BclⅠ区段、19号内含子的HindⅢ相应区段进行DNA测序。结果检出22号内含子倒位携带者1例和倒位者6例;BclⅠPCR/RFLP酶切位点突变患者3例,携带者5例;St14 VNTR家系的连锁分析,发现携带者6例,患者5例;联合诊断家系总阳性率为90.0%;DNA测序两个区段突变位点分析,共发现5种突变。结论采用联合基因诊断方法,对FⅧ基因的3个位点进行联合基因诊断,可提高HA的诊断率及准确率;用PCR-DNA测序法可发现5种突变,并且这些突变位点在国内报道较少,22例患者突变检出率达50.0%。     

PAX6基因5′端非编码区剪接突变能够引起先天性无虹膜症

目的对一先天性无虹膜症家系进行了致病基因PAX6的突变分析。方法PCR反应扩增PAX6基因的所有外显子,PCR产物进行SSCP（单链构象多态性）分析,通过患者与正常人带型的差异来确定突变发生的外显子,对有差异SSCP带型的PCR产物进行直接测序找到突变位点。PCR产物进一步亚克隆到pGEM-T载体,测序验证突变位点。结果发现基因突变为PAX6基因第2内含子和第3外显子之间的剪接识别位点＂AG＂中的碱基A的丢失（IVS2-2delA）。结沦PAX6基因5′端非编码区剪接突变能够引起先天性无虹膜症。     

血友病A患者FVⅢ基因联合诊断及其DNA测序突变分析

目的 探讨血友病A(HA)患者及携带者的基因诊断方法及诊断率.方法 对20例HA患者及家系成员采用长距离PCR扩增(LD-PCR)技术、限制性内切酶酶切位点连锁分析(Bcl I PCR/RFLP)、可变串联重复序列多态性分析(St14 VNTR/PCR);并对FⅧ基因18号内含子的Bcl I区段、19号内含子的HindⅢ相应区段进行DNA测序.结果 检出22号内含子倒位携带者1例和倒位者6例;Bcl I PCR/RFLP酶切位点突变患者3例,携带者5例;St14 VNTR家系的连锁分析,发现携带者6例,患者5例;联合诊断家系总阳性率为90.0%;DNA测序两个区段突变位点分析,共发现5种突变.结论 采用联合基因诊断方法,对FVⅧ基因的3个位点进行联合基因诊断,可提高HA的诊断率及准确率;用PCR-DNA测序法可发现5种突变,并且这些突变位点在国内报道较少,22例患者突变检出率达50.0%.     

七个非综合征型耳聋家系患者的mtDNA A1555G突变性质与特点

目的 探讨非综合征型耳聋家系患者mtDNA A1555G突变性质及其特点,探索临床表型多样性的分子遗传学基础.方法 应用聚合酶链反应-限制性片段长度多态和实时荧光-扩增阻碍突变系统-定量PCR(real time-amplification refractory mutation system-quantitative PCR,RT-ARMS-qPCR)检测7个非综合征型耳聋家系71个成员的mtDNA A1555G突变,并收集、分析其临床资料.结果 7个家系中所有受检的母系成员mtDNA A1555G突变均为阳性,突变性质含同质性和异质性两种;非母系成员及配偶该突变为阴性.7个家系mtDNA A1555G同质性突变的拷贝数与耳聋轻重程度相关(R=0.341,P=0.022);mtDNA A1555G异质性突变的拷贝数与耳聋轻重程度相关(R=0.85,P=0.015).结论 mtDNA A1555G突变可导致非综合征型耳聋和氨基糖甙类抗生素致聋,其突变性质含同质性和异质性两种,且含mtDNA A1555G位点的突变型与野生型的比例与耳聋的严重程度密切相关.     

HLA分型方法进展

HLA分型技术从传统方法发展到基因水平是近年来的一次突破。以限制性片段长度多态性(RFLP)原理探索HLA多态性开始,接着多聚酶链反应(PCR)技术和顺序特异性寡核苷酸(SSO)探针的应用使基因分型方法迅速发展,主要有两方面:PCR结合SSO探针和PCR结合RFLP,两者都在改进中。将PCR与单股构象多态性(SSCP)等结合的方法也在探索中。     

粘多糖贮积症Ⅱ型患者IDS基因的一个新突变

目的　研究粘多糖贮积症 型 ( mucopolysaccharidosis type ,MPS )患者的艾杜糖 - 2 -硫酸酯酶 ( iduronate- 2 - sulfatase,IDS)基因的基因突变。方法　应用聚合酶链反应 -单链构象多态性( polymerase chain reaction- single strand conformation polymorphism,PCR- SSCP)对患者的 IDS基因可能的常见突变第 2、3、5、7～ 9外显子进行检测 ,并对 PCR- SSCP检出的突变进行直接测序 ,测序发现的突变进行 PCR-限制性酶切分析验证。结果　经 PCR- SSCP和 DNA序列分析发现该患者的第 7外显子发生新的点突变 ( G12 5 3T) ;聚合酶链反应 -限制性片段长度多态性 ( PCR- RFL P)电泳检测示患者和母亲出现突变导致的酶切位点 ,进一步验证了序列分析结果。结论　筛查所得的点突变 G12 5 3T可能是该 MPS 患者的致病原因     

粘多糖贮积症Ⅱ型患者艾杜糖-2-硫酸酯酶基因常见突变的检测

目的 探讨并建立粘多糖贮积症Ⅱ型（mucopolysaccharidosis Ⅱ,MPSⅡ)患者艾杜糖－2－硫酸酯酶（iduronate-2-sulphatase,IDS)基因常见突变的检测方法。方法 应用聚合酶链反应－单链构象多态性（polymerase chain reaction-single strand conformation polymorphism,PCR-SSCP）对IDS基因突变热点外显子3、8和9进行点突变检测；应用DNA测序对PCR－SSCP检出的突变进行序列分析；应用聚合酶链反应－限制性片段长度多态性（polymerase chain reaction-restriction fragment length polymorphism,PCR-RFLP)对DNA测序的结果进行检测。结果 以PCR－SSCP发现该患者的IDS基因外显子9有明显异常泳动的条带；DNA测序发现患儿的外显子9发生点突变（C1672T），从而导致患者艾杜糖－2－硫酸酯酶蛋白发生氨基酸替换（R468W）；PCR－RFLP电泳检测结果显示粘多糖贮积症Ⅱ型患者仅出现554bp 1条带，而患儿父母出现257bp和297bp 2条带，进一步验证了序列分析的结果。结论 PCR－SSCP分析、DNA序列分析和PCR－RFLP分析是诊断MPSⅡ的有效方法，三者联合使用可以相互验证、互为补充，提高基因诊断的准确率和成功率。     

47例汉族HIV/AIDS患者外周血白细胞线粒体DNA高变1区序列分析

目的 分析中国汉族HIV-1感染者外周血白细胞线粒体DNA的非编码区的高变1区(HR 1)突变情况,探讨HIV对线粒体影响.方法 分离47例未接受过抗反转录病毒治疗、无机会性感染的HIV/AIDS患者的外周血细胞,提取外周血白细胞DNA,PCR扩增DNA非编码区HR1的大约600 bp的DNA片段,产物纯化后进行测序,测序结果和剑桥序列比对,分析突变位点以及各位点的突变频率.结果 HIV/AIDS患者在非编码HR 1区(核苷酸位点16 024～16 383之间)有124个位点存在多态性,碱基变化率为0～20.47%(中位数为5.33%).大多数突变方式是C→T或T→C的变化.在第16223核苷酸位点,共出现了36个C→T改变,发生率为70.97%(36147);在第16 362核苷酸位点,共出现了26个T→C变化,发生率为55.32%(26147),3个T→G改变,发生率为6.38%(3/47);与以往报道数据类似.结论 HIV-1可能导致线粒体非编码区突变增加.     

Microsatellite instability, mitochondrial DNA large deletions, and mitochondrial DNA mutations in gastric carcinoma

Mitochondrial DNA (mtDNA) large deletions and mtDNA mutations have been demonstrated in various types of human cancer. The relationship between the occurrence of such alterations and the nuclear microsatellite instability (MSI) status of the neoplastic cells remains controversial. In an attempt to clarify the situation in gastric carcinoma, we studied, by PCR/SSCP and sequencing, five mitochondrial genes and two D-loop regions in 32 gastric carcinomas that had been previously screened for MSI and mitochondrial common deletion. MtDNA alterations were detected in 26 carcinomas (81%). All the mtDNA mutations, which occurred mainly in the D-loop and ND1 and ND5 genes, were transitions. D-loop alterations (insertions and/or deletions) were not significantly associated with mutations in the coding regions. There was a trend towards an inverse relationship between the occurrence of mitochondrial common deletion and mtDNA mutations. No significant relationship was observed between MSI status and mtDNA mutations, whereas the mitochondrial common deletion appeared to be almost exclusively restricted to MSI-negative tumors. The latter finding--almost no gastric carcinoma with MSI-positive phenotype has large deletions of mtDNA--needs to be confirmed in a larger series and in tumors from other organs.     

Novel mitochondrial DNA mutations responsible for maternally inherited nonsyndromic hearing loss

Some cases of maternally inherited isolated deafness are caused by mtDNA mutations, frequently following an exposure to aminoglycosides. Two mitochondrial genes have been clearly described as being affected by mutations responsible for this pathology: the ribosomal RNA 12S gene and the transfer RNA serine (UCN) gene. A previous study identified several candidate novel mtDNA mutations, localized in a variety of mitochondrial genes, found in patients with no previous treatment with aminoglycosides. Five of these candidate mutations are characterized in the present study. These mutations are localized in subunit ND1 of complex I of the respiratory chain (m.3388C>A [p.MT-ND1:Leu28Met]), the tRNA for Isoleucine (m.4295A>G), subunit COII of complex IV (m.8078G>A [p.MT-CO2:Val165Ile]), the tRNA of Serine 2 (AGU/C) (m.12236G>A), and Cytochrome B, subunit of complex III (m.15077G>A [p.MT-CYB:Glu111Lys]). Cybrid cell lines have been constructed for each of the studied mtDNA mutations and functional studies have been performed to assess the possible consequences of these mutations on mitochondrial bioenergetics. This study shows that a variety of mitochondrial genes, including protein-coding genes, can be responsible for nonsyndromic deafness, and that exposure to aminoglycosides is not required to develop the disease, giving new insights on the molecular bases of this pathology.     

Novel heteroplasmic frameshift and missense somatic mitochondrial DNA mutations in oral cancer of betel quid chewers

Mitochondrial DNA (mtDNA) has been proposed to be involved in carcinogenesis because of its high susceptibility to oxidative DNA damage and limited repair mechanisms. For investigation of the potential role of somatic mtDNA mutations in the tumorigenesis of oral cancer, we screened the occurrence of mtDNA mutations by the temporal temperature gradient gel electrophoresis method. We amplified the entire mitochondrial genome by use of 32 pairs of overlapping primers, and to identify the mutations, we sequenced DNA fragments showing different banding patterns between normal and tumor mtDNA. Fourteen of eighteen (77.8%) oral carcinomas displayed somatic mtDNA mutations, with a total of 26 mutations. Among them, six were in the mRNA coding region. Three were missense mutations (C14F, H186R, T173P) in NADH dehydrogenase subunit 2, and one was a frameshift mutation, 9485delC, in cytochrome c oxidase subunit III. Eight (44%) tumors had insertion or deletion mutations in the nucleotide position 303-309 poly C region of the D-loop. Multiple large deletions were also observed. Our results demonstrate that somatic mtDNA mutations occur in oral cancer. Some missense and frameshift mutations may play an important role in the tumorigenesis of this carcinoma. More extensive biochemical and molecular studies will be necessary for determining the pathologic effect of these somatic mutations.     

Number of somatic mutations in the mitochondrial D-loop region indicates poor prognosis in breast cancer, independent of TP53 mutation

The objective of this study was to investigate whether somatic mutations in the mitochondrial DNA (mtDNA) D-loop region correlate with known prognostic factors, namely, age, tumor size, lymph node status, metastasis, tumor-node-metastasis stage, lymphovascular invasion, and status of the progesterone receptor, estrogen receptor, ERBB2 (alias HER2/neu), and TP53 proteins (as determined by immunohistochemistry) and to investigate their relationship, if any, to TP53 mutations in human breast cancer. Thirty breast tumors without BRCA mutation, along with adjacent nontumorous tissues, were genotyped for the mtDNA D-loop region and for the promoter as well as the coding region of the TP53 gene. Clinicopathological parameters were recorded and assessed. In all, 17 somatic mtDNA D-loop mutations were identified, in 13 of 30 tumor samples (43%); two mutations were novel: 544C>T and 16510A>C. Four TP53 mutations were found in six tumor samples (20%), and two (c.437G>A and c.706T>C) were novel. Only progesterone receptor status correlated with the number of somatic mtDNA D-loop mutations (likelihood chi-square test; P < 0.05). Somatic mutations in the mtDNA D-loop and in TP53 were independent of each other (Fisher's exact test; P > 0.05). These results suggest that the number of somatic mtDNA D-loop mutations may be an indicator of poor prognosis through a mechanism independent of TP53.     

Mitochondrial DNA D-loop in pancreatic cancer: somatic mutations are epiphenomena while the germline 16519 T variant worsens metabolism and outcome

We ascertained the frequency of mitochondrial DNA (mtDNA) D-loop region somatic mutations in pancreatic cancer (PC) and verified whether polymorphisms were linked to diagnosis, prognosis, and PC-associated diabetes mellitus (DM) in 99 PC cases, 42 chronic pancreatitis (CP) cases, 18 pancreatobiliary tract tumors, and 87 healthy control subjects (CSs). Tissue samples were obtained from 19 patients with PC and 5 with CP. The D-loop region was sequenced from all tissue samples and from blood DNA of the same patients and 12 CSs. D-loop somatic mutations were found in 3 PC tissue samples (16%). Four single nucleotide polymorphisms (SNPs; T152C, T16189C, T16519C, A73G), more frequently found in PC than in CS, were analyzed by denaturing high-performance liquid chromatography-restriction fragment length polymorphism using blood DNA as the starting template in all cases. The T allele of 16519 SNP correlated with DM. The survival of patients with PC correlated with tumor stage and grade and with DM at diagnosis. When survival analysis was performed considering only patients with locally advanced disease, the T allele of mtDNA 16519 SNP correlated with shorter life expectancy. mtDNA D-loop somatic mutations, rarely found in PC, cannot be considered causative events for this tumor type and probably are epiphenomena; the mtDNA D-loop 16519 variant, which worsens PC prognosis, seems to be a predisposing genetic factor for DM.     

Gene organization of the Peking duck mitochondrial genome

Summary The gene organization of the Peking duck mitochondrial (mt)DNA has been deduced through heterologous hybridization using different cloned fragments of the chicken or Japanese quail mitochondrial genome as probes. As in the chicken, and other gallinaceous birds, the Peking duck mtDNA displays a novel gene order which differs from that of other vertebrates by the unusual localization of the tRNA^Glu and ND6 genes next to the displacement (D) loop region of the molecule. The position of these genes with respect to the mitochondrial D-loop region, the cytochrome oxidase subunits I, II and III, the NADH dehydrogenase subunit I and the ribosomal (r) RNAs, was confirmed by the partial nucleotide sequence of cloned mtDNA fragments.     

Mitochondrial DNA mutations and mitochondrial DNA depletion in breast cancer

Somatic mutations in mitochondrial DNA (mtDNA) have been demonstrated in various tumors, including breast cancer. However, it still remains unclear whether the alterations in mtDNA are related to the clinicopathological features and/or the prognosis in the breast cancer. We analyzed somatic mutations in the D-loop region, the common 4,977-bp deletion, and the copy number of mtDNA in breast cancer and paired nontumorous breast tissues from 60 Taiwanese patients. We found that 18 of the 60 (30%) breast cancers displayed somatic mutations in mtDNA D-loop region. The incidence of the 4,977-bp deletion in nontumorous breast tissues (47%) was much higher than that in breast cancers (5%). The copy number of mtDNA was significantly decreased in 38 of the 60 (63%) breast cancers as compared to their corresponding nontumorous breast tissues (P = 0.0008). The occurrence of D-loop mutations was associated with an older onset age (>or=50 years old, P = 0.042), and tumors that lacked expressions of estrogen receptor and progesterone receptor (P = 0.024). Patients with mtDNA D-loop mutation and breast cancer had significantly poorer disease-free survival than those without mutation, when assessed by Kaplan-Meier curves and log-rank test (P = 0.005). Multivariate Cox regression analysis indicated that a D-loop mutation is a significant marker that is independent of other clinical variables and that it can be used to assess the prognosis of patients. Our findings suggest that somatic mutations in mtDNA D-loop can be used as a new molecular prognostic indicator in breast cancer.     

Functional analysis of six androgen receptor mutations identified in patients with partial androgen insensitivity syndrome

Partial androgen insensitivity syndrome (PAIS) is caused by defects in the androgen receptor gene and presents with a wide range of undervirilization phenotypes. We studied the consequences of six androgen receptor ligand-binding domain mutations on receptor function in transfected cells. The mutations, Met742Ile, Met780Ile, Gln798Glu, Arg840Cys, Arg855His and Ile869Met, were identified in PAIS patients with phenotypes representing the full spectrum seen in this condition. In all cases the androgen receptor was found to be defective, suggesting that the mutation is the cause of the clinical phenotype. The Gln798Glu mutation is exceptional in that it did not cause an androgen-binding defect in our system, although the mutant receptor was defective in transactivation assays. This mutation may affect an aspect of binding not tested, or may be part of a functional subdomain of the ligand-binding domain involved in transactivation. Overall we found milder mutations to be associated with milder clinical phenotypes. There is also clear evidence that phenotype is not solely dependent on androgen receptor function. Some of the mutant receptors were able to respond to high doses of androgen in vitro, suggesting that patients carrying these mutations may be the best candidates for androgen therapy. One such mutation is Ile869Met. A patient carrying this mutation has virilized spontaneously at puberty, so in vivo evidence agrees with the experimental result. Thus a more complete understanding of the functional consequences of androgen receptor mutations may provide a more rational basis for gender assignment in PAIS.      

Mitochondrial DNA somatic mutations (point mutations and large deletions) and mitochondrial DNA variants in human thyroid pathology: a study with emphasis on Hürthle cell tumors

In an attempt to progress in the understanding of the relationship of mitochondrial DNA (mtDNA) alterations and thyroid tumorigenesis, we studied the mtDNA in 79 benign and malignant tumors (43 Hürthle and 36 non-Hürthle cell neoplasms) and respective normal parenchyma. The mtDNA common deletion (CD) was evaluated by semiquantitative polymerase chain reaction. Somatic point mutations and sequence variants of mtDNA were searched for in 66 tumors (59 patients) and adjacent parenchyma by direct sequencing of 70% of the mitochondrial genome (including all of the 13 OXPHOS system genes). We detected 57 somatic mutations, mostly transitions, in 34 tumors and 253 sequence variants in 59 patients. Follicular and papillary carcinomas carried a significantly higher prevalence of non-silent point mutations of complex I genes than adenomas. We also detected a significantly higher prevalence of complex I and complex IV sequence variants in the normal parenchyma adjacent to the malignant tumors. Every Hürthle cell tumor displayed a relatively high percentage (up to 16%) of mtDNA CD independently of the lesion's histotype. The percentage of deleted mtDNA molecules was significantly higher in tumors with D-loop mutations than in mtDNA stable tumors. Sequence variants of the ATPase 6 gene, one of the complex V genes thought to play a role in mtDNA maintenance and integrity in yeast, were significantly more prevalent in patients with Hürthle cell tumors than in patients with non-Hürthle cell neoplasms. We conclude that mtDNA variants and mtDNA somatic mutations of complex I and complex IV genes seem to be involved in thyroid tumorigenesis. Germline polymorphisms of the ATPase 6 gene are associated with the occurrence of mtDNA CD, the hallmark of Hürthle cell tumors.