DNA repair pathways and mitochondrial DNA mutations in gastrointestinal carcinogenesis

This work focuses on the main DNA repair pathways, highlighting their role in gastrointestinal carcinogenesis and the role of mitochondrial DNA (mtDNA), mutations being described in several tumor types, including those of the gastrointestinal tract.The mismatch repair (MMR) system is inherently altered in patients with hereditary non-polyposis colorectal cancer, and plays a role in carcinogenesis in a subset of sporadic colorectal, gastric and esophageal cancers. Alterations in homologous recombination (HR) and non-homologous end-joining (NHEJ) also contribute to the development of pancreatic cancer. Gene polymorphisms of some X-ray cross-complementing (XRCCs), cofactor proteins involved in the base excision repair pathway, have been investigated in relation to gastric, colorectal and pancreatic cancer. Yet only one polymorphism, XRCC1 Arg194Trp, appears to be involved in smoking-related cancers and in early onset pancreatic cancer.Although evidence in the literature indicates that mtDNA somatic mutations play a role in gastric and colorectal carcinogenesis, no sound conclusions have yet been drawn regarding this issue in pancreatic cancer, although an mtDNA variant at 16519 is believed to worsen the outcome of pancreatic cancer patients, possibly because it is involved in altering cellular metabolism.     

Search for mitochondrial DNA mutations in migraine subgroups

It has been suggested that mitochondrial mutations cause migraine(-like) symptoms. The presence of mtDNA mutations (3243, 3271, 11084, and deletions) was investigated in three migraine subgroups (maternally transmitted migraine with and without aura, migrainous infarction, and nonfamilial hemiplegic migraine). No mutations were found. These mutations and deletions probably are not involved in the migraine subgroups studied, although an investigation of other material (e.g., muscle tissue) would have shown this with more certainty.     

线粒体DNA突变与阿尔茨海默病的相关性

阿尔茨海默病(Alzheimerdisease,AD)是一种以进行性痴呆为特征的脑变性疾病,很多研究显示它的病变与脑内的能量代谢衰减有密切关系。线粒体是动物细胞中除细胞核外惟一的含有DNA的细胞器,同时也是细胞活动的能源工厂。线粒体形态及功能的缺陷必将引发一系列的细胞功能失调。近年来研究发现阿尔茨海默病患者的脑细胞中的线粒体形态以及线粒体DNA发生了很大的改变,尤其是线粒体DNA缺失率和突变率都明显高于正常人。有关阿尔茨海默病患者的细胞中线粒体功能改变以及线粒体DNA突变的研究已有较大进展,现作初步阐述。     

DNA microarray analysis for the detection of mutations in hemophilia A

BACKGROUND: Congenital deficiency of factor (F) VIII results in the inherited X-linked bleeding disorder hemophilia A. More than 900 different mutations are reported in the hemophilia A mutation database with the largest number of mutations being single nucleotide substitutions distributed throughout the gene. Complicating the molecular characterization of this disease is the complexity of the F8 gene, the mutational heterogeneity, and technical limitations of the current mutation detection techniques. OBJECTIVE: Development of a DNA oligonucleotide microarray-based technique for F8 gene analysis to detect hemophilia A mutations. METHODS: To construct the oligonucleotide DNA microarray system: a total of 720, one base pair overlapping, 25-mer perfect match probes were designed from six exons of the F8 gene. Twenty-two different F8 gene mutations previously identified by CSGE and DNA sequence analysis were tested by using a loss-of-signal analysis approach. Differentially labeled wild type and hemophilic samples were co-hybridized to the array. Sequence alterations were detected by quantifying relative losses of test sample hybridization signals to the perfectly matched probes. RESULTS: A total of 22 different F8 mutations were tested. To test the sensitivity of the system, a blinded study was performed on 16 of the samples. F8 gene mutations can be detected with 96% efficiency with this microarray system. CONCLUSION: This proof-of-principle study has demonstrated that a F8 DNA microarray platform is an alternative gene mutation analysis approach that has a high sensitivity, and reproducibility. The methodology is, however, expensive and time consuming, and with the reduction in sequencing costs, direct sequencing is now the most cost and time efficient strategy for hemophilia A mutation analysis.     

DNA microarray-based detection of nosocomial pathogenic Pseudomonas aeruginosa and Acinetobacter baumannii

Infection by nosocomial pathogenic bacteria is increasingly becoming a major threat to the patients in the hospital. We have developed a diagnostic DNA microarray for the detection of two important nosocomial pathogens, Pseudomonas aeruginosa and Acinetobacter baumannii. The diagnostic DNA microarray contains the species-specific probes of 15mer oligonucleotides designed based on the sequences of 23S ribosomal DNA. The performance of DNA microarray in diagnosing P. aeruginosa and A. baumannii was evaluated using reference bacteria as well as clinical specimens such as blood, stool, pus, sputum, urine and cerebrospinal fluid. Using this DNA microarray, A. baumannii could be successfully detected in 11 out of 13 clinical specimens, thus giving the sensitivity of 84.6% with the specificity of 100% and the positive predictive value of 100%. P. aeruginosa could also be detected in 25 out of 26 clinical specimens, showing the sensitivity of 96.2%, the specificity of 100%, and the positive predictive value of 100%. These results suggest that two nosocomial pathogens, P. aeruginosa and A. baumannii, can be efficiently diagnosed by using the DNA microarray developed in this study.     

Study of mitochondrial DNA mutations in patients with migraine with prolonged aura

Ten patients with migraine with prolonged aura were studied for the presence of mitochondrial DNA point mutations utilizing DNA isolated from blood and hair samples. We analyzed for nine point mutations reported in patients with MELAS (A3243G, C3256T, T3271C, T3291C, A5814G, T8356C, T9957C, G13513A, and A13514G) and three secondary LHON mutations (T4216C, A4917G, and G13708A). None of the patients tested had any of these mutations in mitochondrial DNA. However, one patient was found to have a tRNA(Gln) A4336G mitochondrial DNA variant. From this study it appears that migraine with prolonged aura is not an oligosymptomatic form of MELAS and is not related to secondary LHON mutations. The significance of the tRNA A4336G variant is unknown.     

The specificity of pilin DNA sequences for the detection of pathogenic Neisseria

A nucleic acid hybridization assay for the detection of the pilin gene of Neisseria gonorrhoeae has been devised. The method involves solution hybridization of pilin specific synthetic oligonucleotide probes to genomic DNA in crude cell lysates. This is followed by capture of the probe-target complex onto a microtitre dish well, signal amplification and labelling based on horseradish peroxidase conjugated to oligonucleotides. Detection is achieved with a chemiluminescent enzyme substrate. With a detection limit of about 20,000 cells, the 4-h assay is as sensitive as a radioactive dot-blot method. Over 150 strains of Neisseria gonorrhoeae collected from a variety of sources were detected with the assay. Several N. meningitidis serogroups were also found to react positively. No reactivity was observed with non-pathogenic Neisseria spp. or with other known pathogenic or normal microbial inhabitants of the human urogenital tract.     

SCID mice containing muscle with human mitochondrial DNA mutations. An animal model for mitochondrial DNA defects.

Defects of the mitochondrial genome are important causes of disease. Despite major advances in our investigation of patients, there is no effective therapy. Progress in this area is limited by the absence of any animal models in which we can evaluate treatment. To develop such a model we have injected human myoblasts into the tibialis anterior of SCID mice after inducing necrosis. After injection of normal human myoblasts, regenerating fibers expressed human beta-spectrin, confirming they were derived from fusion of human myoblasts. The stability of the muscle fibers was inferred by demonstrating the formation of motor end plates on the regenerating fibers. In addition, we show the presence of human cytochrome c oxidase subunit II, which is encoded by the mitochondrial genome, in the regenerated fibers. After injection of human myoblasts containing either the A8344G or the T8993C heteroplasmic mitochondrial DNA mutations, human beta-spectrin positive fibers were found to contain the mutation at a similar level to the injected myoblasts. These studies highlight the potential value of this model for the study of mitochondrial DNA defects.     

中国家族性糖尿病人群中线粒体基因突变筛查

目的:国外有研究发现线粒体tRNAGlu基因mt14709T→C突变和tRNASer基因mt12258C→A突变可能与糖尿病发病有关,但该突变是否与中国人群糖尿病发病相关尚未见报道.调查该突变在中国人家族性糖尿病人群中的发生率,并分析其与糖尿病发病的关系.方法:①实验对象:于2004-08/2006-05从上海市糖尿病研究所建立的"中国糖尿病家系库"中选取无亲缘关系的糖尿病家系先证者770例,另外选择同期该研究所收集的无亲缘关系的309例正常人作为正常对照组,纳入对象均为汉族人,均对实验目的知情同意,且得到医院伦理道德委员会批准.②实验方法:采用聚合酶链反应-限制性片段长度多态性方法结合基因直接测序方法检测tRNAGlu基因mt14709T→C和tRNASer基因mt12258C→A突变.③实验评估:收集两组观察对象的年龄、体质量指数、胰岛素抵抗指数等临床资料,并进行比较分析.结果:①在家族性糖尿病组中发现9例(1.17%)mt14709T→C突变,在正常对照组中发现5例(1.62%),两组间mt14709T→C突变发生率差异无显著性意义(χ2=0.348,P =0.56).两组均未发现mt12258C→A突变.②家族糖尿病组中mt14709T→C突变携带者和非携带者之间临床特点(年龄、体质量指数、胰岛素抵抗指数)差异无显著性意义(P＞0.05).结论:线粒体tRNAGlu基因mt14709T→C突变和mt12258C→A突变可能均不是中国人线粒体糖尿病发病的致病原因,其中tRNAGlu基因mt14709T→C突变是中国人线粒体的一种基因多态.     

Site-specific somatic mitochondrial DNA point mutations in patients with thymidine phosphorylase deficiency

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an autosomal recessive disorder caused by loss-of-function mutations in the gene encoding thymidine phosphorylase (TP). This deficiency of TP leads to increased circulating levels of thymidine (deoxythymidine, dThd) and deoxyuridine (dUrd) and has been associated with multiple deletions and depletion of mitochondrial DNA (mtDNA). Here we describe 36 point mutations in mtDNA of tissues and cultured cells from MNGIE patients. Thirty-one mtDNA point mutations (86%) were T-to-C transitions, and of these, 25 were preceded by 5'-AA sequences. In addition, we identified a single base-pair mtDNA deletion and a TT-to-AA mutation. Next-nucleotide effects and dislocation mutagenesis may contribute to the formation of these mutations. These results provide the first demonstration that alterations of nucleoside metabolism can induce multiple sequence-specific point mutations in humans. We hypothesize that, in patients with TP deficiency, increased levels of dThd and dUrd cause mitochondrial nucleotide pool imbalances, which, in turn, lead to mtDNA abnormalities including site-specific point mutations.     

湖北汉族人群2型糖尿病患者线粒体基因突变检测及临床意义

目的研究线粒体DNA(mtDNA)16S rRNA基因(T3200C、C3206T)和ND1基因(A4136G、A4164G和T4216C)突变在湖北汉族2型糖尿病人群中的发生率及临床意义。方法采用等位基因特异性PCR(AS-PCR)、PCR-限制性酶切片段长度多态性(PCR-RFLP)分析及PCR产物直接测序,对175例2型糖尿病患者和200例正常对照的线粒体基因突变进行检测,并用Primer、Antherprot和Mfold软件对检出的突变位点进行分析,对RNA突变后最小自由能下的二级结构变化和ND1基因突变后蛋白质的二级结构改变进行预测。结果2型糖尿病组检出3200(T→C)突变2例(1．14％),3206(C→T)突变11例(6．28％),4216(T→C)突变3例(1．71％),4136位点未发现突变。发现2个未曾报道的新突变位点4164(A→G)7例(4．00％),4200(A→T)1例(0．57％)。对照组中检出3206(C→T)突变8例(3．92％),4164(A→G)突变5例(2．45％),两位点突变率在两组中比较差异无显著性(P>0．05)。RNA二级结构预测显示3200(T→C)突变引起16S rRNA基因最小自由能和二级结构的改变,可能引起疾病。4164(A→G)和4200(A→T)突变分别为Met和Leu的无义突变,4216(T→C)突变可使线粒体呼吸链中一个中性酪氨酸被亲水性组氨酸取代,蛋白质二级结构预测显示该突变可引起NDl蛋白质二级结构改变。研究还显示线粒体基因突变率在≥40岁个体呈上升趋势。结论mtDNA 3200(T→C)和4216(T→C)突变可能增加糖尿病的易感性;3206(C→T)和4164(A→G)为基因多态性改变;4136位点未发现突变。以上结果提示糖尿病的发生在线粒体基因突变上存在一定的异质性。     

Detection of DNA mutations associated with mitochondrial diseases by Agilent 2100 bioanalyzer

BACKGROUND: Molecular analysis of mitochondrial DNA (mtDNA) has provided a final diagnosis for many of the mitochondrial diseases. We evaluated the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA) to determine whether the system could replace the conventional restriction fragment length polymorphism (RFLP) analysis by the agarose gel electrophoresis for the detection of the mtDNA mutation. METHODS: Three members of a family with MELAS syndrome and four members of a family with MERRF syndrome were recruited for this study. After PCR and restriction enzyme digestion, DNA fragments were separated on the Agilent 2100 bioanalyzer in conjunction with the DNA 500 and DNA 1000 Labchip kits and by electrophoresis on precast 3% agarose gels. RESULTS: The data generated by the DNA 500 and DNA 1000 assays using the Agilent 2100 bioanalyzer showed a lower percentage error and a better reproducibility as compared to those obtained by the conventional method. CONCLUSION: Based on the performance of the bioanalyzer, we suggest that this novel Labchip is adequate to replace the current RFLP analysis by the agarose gel electrophoresis for mtDNA mutation detection.     

Real-time detection and quantification of mitochondrial mutations with oligonucleotide primers containing locked nucleic acid

BACKGROUND: The phenotypic expression of disorders caused by point mutations, deletions or depletions within the mitochondrial genome (mtDNA) is heterogeneous. This relates to the phenomena of heteroplasmy, tissue threshold as well as the distribution of mutant DNA among tissues. Hence, the diagnostics of these disorders demands highly specific, sensitive and quantitative methods. METHODS: We have developed an allele-specific quantitative real-time PCR method for the detection of two of the most prevalent disease causing mitochondrial mutations, m.3243A>G (MELAS) and m.8993T>G (NARP). Locked Nucleic Acid (LNA) modified primers were used to obtain high allele specificity. In order to monitor mtDNA depletion a real-time method for mtDNA/nuclear DNA copy number ratio determination was developed. RESULTS: Rapid and sensitive detection and quantification of MELAS and NARP mtDNA alleles were achieved. Heteroplasmy levels as low as 0.01% could be detected, and the mtDNA/nuclear DNA ratio could be determined. CONCLUSIONS: The present method that allows simultaneous determination of heteroplasmy levels and mtDNA/nuclear DNA copy number ratio, will provide a useful tool in molecular diagnostics and in future epidemiological studies of mitochondrial diseases.     

Evaluation of TERT promoter mutations in urinary cell-free DNA and sediment DNA for detection of bladder cancer

BackgroundCell-free DNA (cfDNA) is proposed to be a valuable source of biomarkers in liquid biopsies for various diseases as it is supposed to partially originate from tumor cells. However, data about the diagnostic implications of cfDNA in urine for the detection of bladder cancer (BCa) is sparse.MethodsWe evaluated the usability of urinary cfDNA for diagnostic purposes compared to urine sediment DNA (sDNA) in 53 BCa patients and 36 control subjects by analyzing two abundant point-mutations (C228T/C250T) in the TERT promoter using Next-Generation Sequencing.ResultsMutations were detected in 77% of the urinary sDNA compared to 63% of the cfDNA samples. Moreover, the TERT mutation allele frequencies (MAF) were highly correlated in cfDNA and sDNA. In comparison, the accuracy of the TERT assay was higher in sDNA (84%) compared to cfDNA or voided urine cytology (both 77%). Interestingly, MAFs from leukocyte-rich urines were higher in cfDNA than in sDNA, indicating a diagnostic advantage of cfDNA in such urines.ConclusionsUrine-based mutation detection has the ability to augment and surpass voided urine cytology as the current gold-standard for the non-invasive detection and surveillance of BCa. The analysis of cell-free DNA provides no general diagnostic advantage compared to urine sediment DNA.     

Copro-PCR based detection of Schistosoma eggs using mitochondrial DNA markers

We report on a sensitive, specific and easy to interpret PCR based diagnostic tool for the detection of Schistosoma japonicum eggs in the faeces of infected mammalian hosts. Primer pairs were designed to amplify regions of the mitochondrial DNA of the parasite. The specificity of the PCR primers was tested using either faecal samples from non-infected hosts or hosts infected with the related schistosome species S. mansoni. Sensitivity was investigated in a study, which differentiated the presence or absence of eggs in faecal samples. PCR results were correlated with analysis of the samples by microscopy. PCR analysis provided a level of sensitivity of 87.7%, while specificity was 100%. The PCR-based assay could detect mitochondrial DNA from as little as 0.3 of a single egg. The overall detection threshold of the PCR test was >or=60 eggs per gram of faeces. Advantages of this technique include the ability to scale-up screening and the reproducibility and simplicity of interpretation of results compared with standard microscopic methods.     

Novel mutations of mitochondrial DNA associated with type 2 diabetes in Chinese Han population

Mitochondrial single nucleotide polymorphisms (mtSNPs) have been reported to associate with type-2 diabetes mellitus (T2DM), but mtSNPs appear to be considerably different among different populations and regions. To determine mtSNPs in Chinese Han patients with T2DM, the entire sequences of the mitochondrial genomes from 72 T2DM Chinese (59 +/- 4 years) and 50 age-matched healthy subjects (controls) in Chongqing region of Western China were directly sequenced and mtSNPs were analyzed. We found that M8, M9, D, G, R and A haplogroups exist in Chinese Han population and the frequency of haplogroup M9 was significantly higher in patients with T2DM than in the controls (p = 0.0006, OR 0.06 [95% CI 0.008-0.476]). MtSNPs T3394C in NADH dehydrogenase subunit 1 (ND1), G4491A in ND2, T16189C and T16519C were found with significantly higher frequency in patients with T2DM than in the controls (T16189C, p = 0.0045; T16519C, p < 0.0001; T3394C, p = 0.0015; G4491A, p = 0.0015). In contrast, the frequency of C5178A in ND2 and A10398G in ND3 was higher in the controls than in patients with T2DM (C5178A, p = 0.014; A10398G, p = 0.0011). Our results indicate that mtSNPs T3394C, G4491A, T16189C and T16519C show susceptible tendency to T2DM and mtSNPs C5178A and A10398G seem to be genetic factors for against T2DM. These mtSNPs determined in our study is useful and could be used for early diagnosis and prevention of T2DM in Chinese Han population.     

吸烟肺癌患者口腔黏膜细胞全线粒体DNA获得性突变分析吸烟/口腔黏膜获得性突变与康复预防

目的了解肺癌患者口腔黏膜mtDNA获得性突变情况,探讨肺癌外细胞的线粒体基因突变与肺癌的关系和作为对肺癌预测的生物学指标的可能性。方法利用时相温度梯度凝胶电泳法对12例肺癌患者(吸烟者10例,非吸烟者2例)口腔黏膜细胞及匹配的血液细胞线粒体DNA进行突变筛选,然后进行测序分析。结果在大部分吸烟患者中(8/9),发现口腔黏膜具有两个以上的获得性突变,而在两个非吸烟的患者仅发现1个突变。在11例(11/12,92%)患者中共发现有26个获得性突变,15个突变发生在高变的D环区(58%),11个在mRNA区(42%)。除303～309位点具有长度不稳定外,未见其他微卫星不稳定和5kb的大范围缺失突变。结论吸烟的肺癌患者口腔黏膜细胞线粒体DNA具有高发生频率的获得性突变。