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Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck.
Wilson IJ, Carling PJ, Alston CL, Floros VI, Pyle A, Hudson G, Sallevelt SC, Lamperti C, Carelli V, Bindoff LA, Samuels DC, Wonnapinij P, Zeviani M, Taylor RW, Smeets HJ, Horvath R, Chinnery PF
(2016) Hum Mol Genet 25: 1031-41
MeSH Terms: Bayes Theorem, Child, DNA, Mitochondrial, Female, Humans, Inheritance Patterns, Mitochondrial Diseases, Models, Genetic, Pedigree, Phenotype, Point Mutation, Polymorphism, Restriction Fragment Length, Publication Bias
Show Abstract · Added February 15, 2016
With a combined carrier frequency of 1:200, heteroplasmic mitochondrial DNA (mtDNA) mutations cause human disease in ∼1:5000 of the population. Rapid shifts in the level of heteroplasmy seen within a single generation contribute to the wide range in the severity of clinical phenotypes seen in families transmitting mtDNA disease, consistent with a genetic bottleneck during transmission. Although preliminary evidence from human pedigrees points towards a random drift process underlying the shifting heteroplasmy, some reports describe differences in segregation pattern between different mtDNA mutations. However, based on limited observations and with no direct comparisons, it is not clear whether these observations simply reflect pedigree ascertainment and publication bias. To address this issue, we studied 577 mother-child pairs transmitting the m.11778G>A, m.3460G>A, m.8344A>G, m.8993T>G/C and m.3243A>G mtDNA mutations. Our analysis controlled for inter-assay differences, inter-laboratory variation and ascertainment bias. We found no evidence of selection during transmission but show that different mtDNA mutations segregate at different rates in human pedigrees. m.8993T>G/C segregated significantly faster than m.11778G>A, m.8344A>G and m.3243A>G, consistent with a tighter mtDNA genetic bottleneck in m.8993T>G/C pedigrees. Our observations support the existence of different genetic bottlenecks primarily determined by the underlying mtDNA mutation, explaining the different inheritance patterns observed in human pedigrees transmitting pathogenic mtDNA mutations.
© The Author 2016. Published by Oxford University Press.
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13 MeSH Terms
Recurrent tissue-specific mtDNA mutations are common in humans.
Samuels DC, Li C, Li B, Song Z, Torstenson E, Boyd Clay H, Rokas A, Thornton-Wells TA, Moore JH, Hughes TM, Hoffman RD, Haines JL, Murdock DG, Mortlock DP, Williams SM
(2013) PLoS Genet 9: e1003929
MeSH Terms: Base Sequence, DNA Replication, DNA, Mitochondrial, Genome, Mitochondrial, Humans, Mitochondria, Muscle, Skeletal, Mutation, Organ Specificity, Polymorphism, Restriction Fragment Length
Show Abstract · Added December 12, 2013
Mitochondrial DNA (mtDNA) variation can affect phenotypic variation; therefore, knowing its distribution within and among individuals is of importance to understanding many human diseases. Intra-individual mtDNA variation (heteroplasmy) has been generally assumed to be random. We used massively parallel sequencing to assess heteroplasmy across ten tissues and demonstrate that in unrelated individuals there are tissue-specific, recurrent mutations. Certain tissues, notably kidney, liver and skeletal muscle, displayed the identical recurrent mutations that were undetectable in other tissues in the same individuals. Using RFLP analyses we validated one of the tissue-specific mutations in the two sequenced individuals and replicated the patterns in two additional individuals. These recurrent mutations all occur within or in very close proximity to sites that regulate mtDNA replication, strongly implying that these variations alter the replication dynamics of the mutated mtDNA genome. These recurrent variants are all independent of each other and do not occur in the mtDNA coding regions. The most parsimonious explanation of the data is that these frequently repeated mutations experience tissue-specific positive selection, probably through replication advantage.
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10 MeSH Terms
Functional PstI/RsaI polymorphism in CYP2E1 is associated with the development, progression and poor outcome of gastric cancer.
Feng J, Pan X, Yu J, Chen Z, Xu H, El-Rifai W, Zhang G, Xu Z
(2012) PLoS One 7: e44478
MeSH Terms: Aged, Case-Control Studies, Cytochrome P-450 CYP2E1, Deoxyribonucleases, Type II Site-Specific, Disease Progression, Female, Gene Expression Regulation, Neoplastic, Genotype, Homozygote, Humans, Male, Middle Aged, Models, Genetic, Odds Ratio, Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, Prognosis, Regression Analysis, Stomach Neoplasms, Treatment Outcome
Show Abstract · Added September 3, 2013
BACKGROUND - Cytochrome P450 2E1 (CYP2E1), an ethanol-inducible enzyme, has been shown to metabolically activate various carcinogens, which is critical for the development and progression of cancers. It has demonstrated that CYP2E1 polymorphisms alter the transcriptional activity of the gene. However, studies on the association between CYP2E1 polymorphisms (PstI/RsaI or DraI) and gastric cancer have reported conflicting results. Thus, the aim of the present study was to investigate whether CYP2E1 polymorphisms is associated with the development and progression of gastric cancer and its prognosis in Chinese patients.
METHODS - A case-control study was conducted in which CYP2E1 PstI/RsaI and DraI polymorphisms were analyzed in 510 Chinese patients with gastric cancer and 510 age- and sex- matched healthy controls by PCR-RFLP. Odds ratios were estimated by multivariate logistic regression, and the lifetime was calculated by Kaplan-Meier survival curves. In addition, a meta-analysis was also conducted to verify the findings.
RESULTS - For CYP2E1 PstI/RsaI polymorphism, C2C2 homozygotes (OR = 2.15; CI: 1.18-3.94) and C2 carriers (OR = 1.48; CI: 1.13-1.96) were associated with an increased risk of gastric cancer when compared with C1C1 homozygotes. Both C1C2 and C2C2 genotypes were associated with advanced stage, but not the grade of gastric cancer. Moreover, C2C2 genotype was identified as an independent marker of poor overall survival for gastric cancer. However, there was not any significant association between CYP2E1 DraI polymorphism and the risk of gastric cancer. In the meta-analysis, pooled data from 13 studies confirmed that the CYP2E1 PstI/RsaI polymorphism was associated with a significantly increased risk of gastric cancer.
CONCLUSION - CYP2E1 PstI/RsaI polymorphism is associated with increased risk of development, progression and poor prognosis of gastric cancer in Chinese patients. Pooled data from 13 studies, mainly in Asian countries, are in agreement with our findings.
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20 MeSH Terms
Pathway analyses identify TGFBR2 as potential breast cancer susceptibility gene: results from a consortium study among Asians.
Ma X, Beeghly-Fadiel A, Lu W, Shi J, Xiang YB, Cai Q, Shen H, Shen CY, Ren Z, Matsuo K, Khoo US, Iwasaki M, Long J, Zhang B, Ji BT, Zheng Y, Wang W, Hu Z, Liu Y, Wu PE, Shieh YL, Wang S, Xie X, Ito H, Kasuga Y, Chan KY, Iwata H, Tsugane S, Gao YT, Shu XO, Moses HL, Zheng W
(2012) Cancer Epidemiol Biomarkers Prev 21: 1176-84
MeSH Terms: Adult, Breast, Breast Neoplasms, Case-Control Studies, China, Female, Genetic Predisposition to Disease, Humans, Middle Aged, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, Polymorphism, Single Nucleotide, Prognosis, Protein-Serine-Threonine Kinases, Receptor, Transforming Growth Factor-beta Type II, Receptors, Transforming Growth Factor beta, Risk Factors, Signal Transduction
Show Abstract · Added February 17, 2014
BACKGROUND - The TGF-β signaling pathway plays a significant role in the carcinogenic process of breast cancer.
METHODS - We systematically evaluated associations of common variants in TGF-β signaling pathway genes with breast cancer risk using a multistage, case-control study among Asian women.
RESULTS - In the first stage, 341 single-nucleotide polymorphisms with minor allele frequencies ≥ 0.05 across 11 genes were evaluated among 2,926 cases and 2,380 controls recruited as a part of the Shanghai Breast Cancer Genetics Study (SBCGS). In the second stage, 20 SNPs with promising associations were evaluated among an additional 1,890 cases and 2,000 controls from the SBCGS. One variant, TGFBR2 rs1078985, had highly consistent and significant associations with breast cancer risk among participants in both study stages, as well as promising results from in silico analysis. Additional genotyping was carried out among 2,475 cases and 2,343 controls from the SBCGS, as well as among 5,077 cases and 5,384 controls from six studies in the Asian Breast Cancer Consortium (stage III). Pooled analysis of all data indicated that minor allele homozygotes (GG) of TGFBR2 rs1078985 had a 24% reduced risk of breast cancer compared with major allele carriers (AG or AA; OR, 0.76; 95% CI, 0.65-0.89; P = 8.42 × 10(-4)).
CONCLUSION - These findings support a role for common genetic variation in TGF-β signaling pathway genes, specifically in TGFBR2, in breast cancer susceptibility.
IMPACT - These findings may provide new insights into the etiology of breast cancer as well as future potential therapeutic targets.
©2012 AACR
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18 MeSH Terms
Effect of recipient-derived cells on the progression of familial amyloidotic polyneuropathy after liver transplantation: a retrospective study.
Ohya Y, Jono H, Nakamura M, Hayashida S, Ueda M, Obayashi K, Misumi S, Asonuma K, Ando Y, Inomata Y
(2010) Ann Clin Biochem 47: 529-34
MeSH Terms: Adult, Amyloid Neuropathies, Familial, Amyloidogenic Proteins, Chromosomes, Human, X, Chromosomes, Human, Y, Female, Humans, In Situ Hybridization, Fluorescence, Liver, Liver Transplantation, Male, Middle Aged, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, Prealbumin, Retrospective Studies, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Show Abstract · Added February 11, 2015
BACKGROUND - Some familial amyloidotic polyneuropathy (FAP) patients show the post-transplant progression of the clinical symptoms. Although the presence of recipient-derived cells in transplanted livers has been reported, no studies investigating the functional significance of this post-transplant chimerism in transplanted FAP patients were performed. The aims of this study were to evaluate amyloidogenic transthyretin (ATTR) production of recipient-derived cells and the relationship between the protein from recipient-derived cells and the progression of FAP symptoms after liver transplantation (LT).
METHODS - Seven FAP ATTR Val30Met patients who underwent LT were included in this study. In one male patient with sex-mismatched donor, fluorescence in situ hybridization (FISH) method was performed on a liver biopsy sample using DNA probes for visualizing X and Y chromosomes to detect the recipient-derived cells. In three patients including the FISH-analysed patient, ATTR mRNA expression in transplanted livers was evaluated by the polymerase chain reaction (PCR)-restriction fragment length polymorphism method and realtime quantitative reverse transcription-PCR. In five of the seven patients, ATTR in serum protein expression was measured by mass spectrometry.
RESULTS - One FAP patient has 3.1% recipient-derived cells in the transplanted liver. The ATTR mRNA was not expressed in any of the three transplanted livers. The ATTR was not detected in any sera of the sampled patients.
CONCLUSION - Although the FAP patient had recipient-derived cells in the transplanted liver, the recipient-derived cells did not contribute to the production of ATTR in our specific case. The effect of recipient-derived cells on the post-transplant progression of FAP symptoms may be negligible.
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17 MeSH Terms
Mutations in the mitochondrial DNA D-loop region and breast cancer risk.
Ye C, Shu XO, Pierce L, Wen W, Courtney R, Gao YT, Zheng W, Cai Q
(2010) Breast Cancer Res Treat 119: 431-6
MeSH Terms: Adult, Breast Neoplasms, Case-Control Studies, China, DNA, Mitochondrial, Female, Genetic Predisposition to Disease, Humans, Logistic Models, Middle Aged, Mutation, Nucleic Acid Conformation, Odds Ratio, Polymorphism, Restriction Fragment Length, Risk Assessment, Risk Factors
Show Abstract · Added March 18, 2014
Mitochondrial genome alterations have been suggested to play an important role in carcinogenesis. The D-loop region of mitochondrial DNA (mtDNA) contains essential transcription and replication elements, and mutations in this region may serve as a potential sensor for cellular DNA damage and a marker for cancer development. Using data and samples from the Shanghai Breast Cancer Study, we investigated MnlI restriction sites located between nucleotides 16,106 and 16,437 of the mtDNA D-loop region to evaluate restriction fragment length polymorphism (RFLP) patterns in tumor tissue from 501 primary breast cancer patients when compared with tumor tissue from 203 women with benign breast disease (BBD). RFLP patterns in correspondingly paired, adjacent, non-tumor tissues taken from 120 primary breast cancer patients and 59 BBD controls were also evaluated. Five common RFLP patterns were observed, and no significant differences were observed in the distribution of these patterns between tumor and adjacent non-tumor tissue samples from breast cancer patients and tissue samples from BBD controls. On the other hand, somatic MnlI site mutations, defined as a difference in MnlI RFLP pattern between tumor tissue and the corresponding, adjacent, non-tumor tissue, occurred more frequently in breast cancer patients (28.3%) than in BBD patients (15.3%) (P = 0.05) and more frequently in proliferative BBD (13.0%) than in non-proliferative BBD (7.1%). Our data suggest that somatic MnlI site mutations may play a role in the pathogenesis of breast cancer.
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16 MeSH Terms
Acquired resistance to epidermal growth factor receptor kinase inhibitors associated with a novel T854A mutation in a patient with EGFR-mutant lung adenocarcinoma.
Bean J, Riely GJ, Balak M, Marks JL, Ladanyi M, Miller VA, Pao W
(2008) Clin Cancer Res 14: 7519-25
MeSH Terms: Adenocarcinoma, Afatinib, Aged, Amino Acid Sequence, Antineoplastic Agents, Base Sequence, Cell Line, Tumor, Drug Resistance, Neoplasm, ErbB Receptors, Erlotinib Hydrochloride, Female, Gefitinib, Humans, Immunoblotting, Lung Neoplasms, Molecular Sequence Data, Mutation, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, Protein Kinase Inhibitors, Protein Structure, Quaternary, Quinazolines, Sequence Alignment
Show Abstract · Added March 24, 2014
PURPOSE - Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are associated with sensitivity of lung adenocarcinomas to the EGFR tyrosine kinase inhibitors, gefitinib and erlotinib. Acquired drug resistance is frequently associated with a secondary somatic mutation that leads to the substitution of methionine for threonine at position 790 (T790M). We aimed to identify additional second-site alterations associated with acquired resistance.
EXPERIMENTAL DESIGN - Tumor samples were obtained from 48 patients with acquired resistance. Tumor cell DNA was analyzed for EGFR kinase domain mutations. Molecular analyses were then done to characterize the biological properties of a novel mutant EGFR allele.
RESULTS - A previously unreported mutation in exon 21 of EGFR, which leads to substitution of alanine for threonine at position 854 (T854A), was identified in one patient with a drug-sensitive EGFR L858R-mutant lung adenocarcinoma after long-term treatment with tyrosine kinase inhibitors. The T854A mutation was not detected in a pretreatment tumor sample. The crystal structure analyses of EGFR suggest that the T854 side chain is within contact distance of gefitinib and erlotinib. Surrogate kinase assays show that the EGFR T854A mutation abrogates the inhibition of tyrosine phosphorylation by erlotinib. Such resistance seems to be overcome by a new irreversible dual EGFR/HER2 inhibitor, BIBW 2992.
CONCLUSIONS - The T854A mutation is the second reported second-site acquired resistance mutation that is within contact distance of gefitinib and erlotinib. These data suggest that acquired resistance to ATP-mimetic EGFR kinase inhibitors may often be associated with amino acid substitutions that alter drug contact residues in the EGFR ATP-binding pocket.
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23 MeSH Terms
Intragenomic heterogeneity and intergenomic recombination among Vibrio parahaemolyticus 16S rRNA genes.
Harth E, Romero J, Torres R, Espejo RT
(2007) Microbiology 153: 2640-2647
MeSH Terms: Base Sequence, Cluster Analysis, DNA Fingerprinting, Genes, rRNA, Genetic Variation, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S, Recombination, Genetic, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Shellfish, Vibrio parahaemolyticus
Show Abstract · Added February 15, 2016
Vibrio parahaemolyticus is a marine bacterium bearing 11 copies of ribosomal operons. In some strains, such as RIMD2210633, the genome includes identical copies of 16S rRNA genes (rrs). However, it is known that other strains of the species, such as strains ATCC 17802 and RIMD2210856, show conspicuous intragenomic rrs heterogeneity. The extent and diversity of the rrs heterogeneity in V. parahaemolyticus were studied in further detail by characterization of the rrs copies in environmental isolates belonging to 21 different genotype groups. Thirteen of these groups showed intragenomic heterogeneity, containing altogether 16 sequences differing within a 25 bp segment of their rrs. These sequences grouped into four clusters differing in at least four nucleotide sites. Some isolates contained rrs alleles from up to three different clusters. Each segment sequence conserved the stem-loop characteristic of the 16S rRNA structure of this 25 bp sequence. The double-stranded stem sequence was quite variable, but almost every variation had a compensatory change to maintain seven to eight paired bases. Conversely, the single-strand loop sequence was conserved. The results may be explained as a consequence of recombination among rrs evolving in different bacteria. The results suggest that intergenomic rrs recombination is very high in V. parahaemolyticus and that it occurs solely among Vibrio species. This high rrs homologous intergenomic recombination could be an effective mechanism to maintain intragenomic rrs cohesion, mediating the dispersal of the most abundant rrs version among the 11 intragenomic loci.
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17 MeSH Terms
Clinical phenotypes associated with the complement factor H Y402H variant in age-related macular degeneration.
Brantley MA, Edelstein SL, King JM, Apte RS, Kymes SM, Shiels A
(2007) Am J Ophthalmol 144: 404-408
MeSH Terms: Aged, Case-Control Studies, Choroidal Neovascularization, Complement Factor H, Exons, Female, Fluorescein Angiography, Genetic Variation, Genotype, Humans, Macular Degeneration, Male, Phenotype, Polymorphism, Restriction Fragment Length, Polymorphism, Single Nucleotide, Retrospective Studies, Sequence Analysis, DNA
Show Abstract · Added December 10, 2013
PURPOSE - To determine whether the complement factor H (CFH) Y402H variant is associated with specific age-related macular degeneration (AMD) clinical phenotypes.
DESIGN - Retrospective, case-control study.
METHODS - One hundred and eighty-eight white subjects with AMD and 189 control subjects were genotyped for the T-to-C polymorphism in exon 9 of the CFH gene by restriction-fragment length analysis and deoxyribonucleic acid (DNA) sequencing using genomic DNA from mouthwash samples. AMD phenotypes were characterized by clinical examination, fundus photography, and fluorescein angiography.
RESULTS - Heterozygosity for the at-risk genotype (TC) increased the likelihood for AMD 2.1-fold (95% confidence interval [CI], 1.3 to 3.3), whereas homozygosity for the genotype (CC) increased the likelihood for AMD 6.5-fold (95% CI, 3.4 to 12.5) in our population. The C allele was associated significantly with predominantly classic choroidal neovascularization (odds ratio [OR], 2.01; 95% CI, 1.34 to 3.30). Neovascular lesion size was similar among the three genotypes (P = .67).
CONCLUSIONS - The Y402H CFH variant carried a significantly increased risk for developing AMD in our population. Genotype and phenotype correlations regarding choroidal neovascular lesion type were observed.
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17 MeSH Terms
Recombinase-mediated cassette exchange to rapidly and efficiently generate mice with human cardiac sodium channels.
Liu K, Hipkens S, Yang T, Abraham R, Zhang W, Chopra N, Knollmann B, Magnuson MA, Roden DM
(2006) Genesis 44: 556-64
MeSH Terms: Animals, DNA Primers, DNA, Complementary, Electroporation, Embryonic Stem Cells, Gene Components, Gene Transfer Techniques, Genetic Vectors, Humans, Integrases, Mice, Mice, Transgenic, Models, Animal, Muscle Proteins, NAV1.5 Voltage-Gated Sodium Channel, Polymorphism, Restriction Fragment Length, Reverse Transcriptase Polymerase Chain Reaction, Sodium Channels
Show Abstract · Added February 23, 2011
SCN5A encodes the predominant voltage-gated sodium channel isoform in human heart and nearly 100 variants have now been described and studied in vitro. However, development of animal models to analyze function of such large numbers of human gene variants represents a continuing challenge in translational medicine. Here, we describe the implementation of a two stage procedure, recombinase-mediated cassette exchange (RMCE), to efficiently and rapidly generate mice in which a full-length human cDNA replaces expression of the murine ortholog. In the first step of RMCE, conventional homologous recombination in mouse ES cells was used to replace scn5a exon 2 (that contains the translation start site) with a cassette acceptor that includes the thymidine kinase gene, flanked by loxP/inverted loxP sites. In the second step, the cassette acceptor site was replaced by the full-length wild-type human SCN5A cDNA by Cre/loxP-mediated recombination. The exchange event occurred in 7/29 (24%) colonies, and the time from electroporation to first homozygotes was only 8 months. PCR-restriction fragment length polymorphism (RFLP) showed that the murine isoform was replaced by the human one, and functional studies indicated that mice with human cardiac sodium channels have wild-type sodium current density, action potential durations, heart rates, and QRS durations. These data demonstrate that RMCE can be used to generate mice in which a targeted allele can be rapidly and efficiently replaced by variants of choice, and thereby can serve as an enabling approach for the functional characterization of ion channel and other DNA variants.
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18 MeSH Terms