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Results for “Genome mutation”

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At least 721 records · Page 40Linked to original sources
PubMed1986

Fixation of mutations in the viral genome during an outbreak of foot-and-mouth disease: heterogeneity and rate variations.

Rates of fixation of mutations during the evolution of the foot-and-mouth disease virus (FMDV) C1 in nature have been estimated by hybridization of viral RNA to cloned cDNAs representing defined FMDV genome segments, and comparison of the selected RNAs by T1 RNase oligonucleotide fingerprinting. Values ranged from less than 0.04 X 10(-2) to 4.5 X 10(-2) substitutions per nucleotide per year (s/nt/yr), depending on the time period and the genomic segment considered. Rates for viral structural protein genes were up to sixfold higher than for nonstructural protein genes. Values in excess of 10(-2) s/nt/yr have been measured for the RNA region that encodes VP1-VP3. The nucleotide sequences of the major immunogenic region of capsid protein VP1 have been determined for six new FMDV C1 isolates, and they are compared with the two previously known sequences of FMDV C1 (C-S8 and C1-O). Both oligonucleotide fingerprinting of selected RNA fragments and direct nucleotide sequencing demonstrate that genetic heterogeneity exists among three viruses isolated on the same day, introducing a significant indetermination in the evaluation of fixation rates of mutations. During the FMDV C1 outbreak, amino acid substitutions did occur that are known to affect the immunological properties of the virus. The proportion of mutations between two viral RNAs does not increase significantly with the time elapsed between the two isolations, suggesting a cocirculation of multiple, related, nonidentical FMDVs ('evolving quasispecies') as the mode of evolution of this agent.

Amino Acid Sequence↗
PubMed2006

Contribution of somatic mutations in the mitochondrial genome to the development of cancer and tolerance against anticancer drugs.

Mitochondrial defects have long been suspected to play an important role in the development of cancer. Although most cancer cells harbor somatic mutations in mitochondrial DNA (mtDNA), the question of whether such mutations positively contribute to the development of cancer remained unclear. To clarify the role of mutant mtDNA excluding effects by the nuclear background, we focus on a method of transmitochondrial cybrids. Tumors were formed by transplanting cybrids with or without mutant mtDNA into nude mice and compared each size, revealing that mutant cybrids enhanced tumorigenesis. Next, we discuss a method for excluding the possibility of secondary nuclear mutations that may affect tumorigenesis. Mitochondrial genes that had been converted from mitochondrial to nuclear codons and equipped with a mitochondrial-targeting sequence were introduced into the nucleus of mutant cybrids. The gene products complemented the dysfunction, and reduced the promotion of tumors. By these methods, we concluded that mutant mitochondria positively and directly contribute to tumorigenesis. Since apoptosis occurred less frequently in the mutant versus wild-type cybrids in tumors, pathogenic mtDNA mutations contribute to the promotion of tumors by preventing apoptosis. Finally, we discuss the role of mutant mtDNA in conferring tolerance against anticancer drugs.

Animals↗
PubMed1990

Two unrelated patients with familial hyperproinsulinemia due to a mutation substituting histidine for arginine at position 65 in the proinsulin molecule: identification of the mutation by direct sequencing of genomic deoxyribonucleic acid amplified by polymerase chain reaction.

Mutations in the insulin gene can impair the bioactivity of the insulin molecule. Previously, two classes of mutations have been identified: 1) those that impair posttranslational processing of proinsulin to insulin, and 2) those that alter the structure of the insulin molecule, thereby reducing the affinity of the molecule for the insulin receptor. We have investigated two apparently unrelated patients, both of which have mutations that inhibit the conversion of proinsulin to insulin. By directly sequencing genomic DNA amplified by polymerase chain reaction, we have demonstrated that both patients are heterozygous for the same point mutation converting codon 65 from an arginine (CGT) to a histidine (CAT) codon. Because Arg65 is one of the two dibasic amino acids at the site of proteolytic cleavage between the insulin A-chain and C-peptide, this mutation explains the impairment in the cleavage of proinsulin to insulin. Interestingly, the same His65 mutation has been identified in the insulin gene of a Japanese kindred with familial hyperproinsulinemia. Thus, this mutation has occurred in three apparently unrelated kindreds from two different racial groups. This observation is consistent with the hypothesis that the dinucleotide sequence CpG, the first two nucleotides in the arginine (CGT) codon, is a "hot spot" for mutations.

Alleles↗
PubMed2003

Experimental evolution yields hundreds of mutations in a functional viral genome.

Two lines of the bacteriophage T7 were grown to fix mutations indiscriminately, using a combination of population bottlenecks and mutagenesis. Complete genome sequences revealed 404 and 299 base substitutions in the two lines, the largest number characterized in functional microbial genomes so far. Missense substitutions outnumbered silent substitutions. Silent substitutions occurred at similar rates between essential and nonessential genes, but missense substitutions occurred at a higher rate in nonessential genes than in essential genes, as expected if they were less deleterious in the nonessential genes. Viral fitness declined during this protocol, and subsequent passaging of each mutated line in large population sizes restored some of the lost fitness. Substitution levels during these recoveries were less than 6% of those during the bottleneck phase, and only two changes during recovery were reversions of the original mutations. Exchanges of genomic fragments between the two recovered lines revealed that fitness effects of some substitutions were not additive-that interactions were accumulating which could lead to incompatibility between the diverged genomes. Based on these results, unprecedented high rates of nucleotide and functional divergence in viral genomes should be attainable experimentally by using repeated population bottlenecks at a high mutation rate interspersed with recovery.

Bacteriophage T7↗
PubMed1997

Mutation-selection balance under genomic imprinting at an autosomal locus.

I model the effect of genomic imprinting on the equilibrium allele frequencies at an autosomal diallelic locus subject to viability selection and mutation. The population size is assumed to be very large; male and female mutation rates may be unequal. Different models examine cases of the inactivation of one gene (with both complete and partial penetrance) and of differential expression of genes according to the parent of origin. In the simplest cases the frequency of the deleterious allele is approximately twice that of a dominant nonimprinting mutant, but considerably less than that of a recessive nonimprinting mutant. Under imprinting, selection and unequal mutation rates interact: other things being equal, male-biased mutation leads to lower mutant frequencies under maternal imprinting and higher frequencies under paternal imprinting. I also model cases where just one allele is imprintable (and the other not). These models allow us to predict the frequency of a failure to imprint in a normally imprinting system, as well as the frequency of imprinting at a standard nonimprinting locus.

Animals↗
PubMed2005

Genetic instability of C. elegans comes naturally.

There have been many attempts to measure the genome-wide mutation rate for spontaneous mutations, using measurements of traits in inbred lines in which mutations have accumulated. However, these are likely to miss many small-effect mutations that are important for evolutionary processes. Recently, the genome-wide spontaneous mutation rate in inbred lines of Caenorhabditis elegans was estimated, using DNA sequencing. The results imply that the mutation rate is surprisingly high, and that insertion-deletion mutations are unexpectedly common. Phenotypic assays of the same lines detected only a small proportion of mutations that were predicted to have evolutionarily significant fitness effects.

Animals↗
PubMed1994

Hepatitis may precede the occurrence of precore region mutation in hepatitis B virus genome during infection in young carriers.

To understand when the mutation with a stop codon of precore region in hepatitis B virus genome occurs, the prevalence of the mutation of viral DNA clones propagated from sera of school-age carriers was investigated with respect to hepatitis B e antigen (HBeAg)/anti-HBe and sequential changes of mutants along HBeAg seroconversion were analyzed. Of 32 carriers aged 8-18 years, 14 HBeAg(+) patients had 2.2% mutant clones, whereas 8 patients with low titer anti-HBe had a higher rate of 18.1% (P < 0.01) and the highest rate of 61.3% was found in 10 patients with high anti-HBe titer (P < 0.001). By contrast, the amount of viral DNA decreased significantly in patients with anti-HBe. Sequential analysis in six cases revealed three types of seroconversion with time difference of the emergence and increase of mutant clones. It is concluded that mutation occurs at a relatively young age and increases along time and/or HBeAg seroconversion. Hepatitis might precede or accelerate the emergence and increase of mutant population which might be predictive of sustained resolution of the disease.

Adolescent↗
PubMed2003

[Bacteria of the Burkholderia cepacia complex: specific features of diagnostics, genome organization and metabolism].

Modern data, related with the identification and typing of the complex B. cepacia bacteria, are analyzed in the article by using the poly-phase taxonomic approach. An optimal scheme for identifying and typing the complex B. cepacia bacteria, involving the microbiological and molecular-biological methods of laboratory diagnostics, is presented. The key and assumed factors of pathogenicity of the discussed bacteria are described. The possible phylogenetic relations of the complex B. cepacia bacteria with phytopathgens as well as with pathogenic bacteria of species Burkholderia, Pseudomonas, Escherichia, B. mallei, B. pdeudomallei, P. seruginosa and E. coli are described. A possible role of genome alterations and mutations in the genome of the complex B. cepacia bacteria (with the latter genome having unusual properties, i.e. a big size, and a considerable quantity of insertion sequences) in creating the conditions for the "pulsing" evolution "jerks", i.e. for a rapid change-over from saprophytism in the soil to a pathogenic causative agent of a viral-and-bacteriological infection. Such mechanism can be regarded as a rapid and radical adaptation of a microorganism under the conditions of changing ecological niches.

Adaptation, Physiological↗
PubMed2005

Genetic determinants of cell type-specific poliovirus propagation in HEK 293 cells.

The ability of poliovirus to propagate in neuronal cells can be reduced by introducing appropriate nucleotide substitutions into the viral genome. Specific mutations scattered throughout the poliovirus genome yielded the live attenuated vaccine strains of poliovirus. Neuron-specific propagation deficits of the Sabin strains are partially encrypted within a confined region of the internal ribosomal entry site (IRES), which carries attenuating point mutations in all three serotypes. Recently, high levels of neurovirulence attenuation were achieved with genetically engineered polioviruses containing heterologous IRES elements. This is exemplified with poliovirus recombinants replicating under control of a human rhinovirus type 2 (HRV2) IRES element. We have carried out experiments delineating the genetic basis for neuronal IRES function. Neuronal dysfunction of the HRV2 IRES is determined mainly by IRES stem-loop domain V, the locus for attenuating point mutations within the Sabin strains. Neuronal incompetence associated with HRV2 IRES domain V is substantially more pronounced than that observed with the attenuating IRES point mutation of the Sabin serotype 1 vaccine strain. Mix-and-match recombination of polio and HRV2 IRES domain V suggests that the attenuation phenotype correlates with overall structural features rather than primary sequence. Our experiments have identified HEK 293 cells as a novel system for the study of neuron-specific replication phenotypes of poliovirus. This cell line, originally derived from embryonic human kidney, has recently been described to display neuronal characteristics. We report propagation properties in HEK 293 cells for poliovirus recombinants with attenuated neurovirulence in experimental animals that corroborate this observation.

Amino Acid Sequence↗
PubMed1997

Expression genetics in cancer: shifting the focus from DNA to RNA.

Expression genetics is a conceptually different approach to the identification of cancer-related genes than the search for mutations at the genome level. While mutations lie at the heart of cancer, at least in its early stages, what is recognized here are phenotypic changes usually many steps removed from the initiating mutation. Classically cancer geneticists have concentrated on genomic changes and have ignored the productive potential of examining downstream events based on screening for differential gene expression between tumor cells and well matched normal counterparts. Genes involved in cancer affect the normal functions of many cellular processes: not only proliferation but cell-cell and cell-matrix interactions, DNA repair, invasion and motility, angiogenesis, senescence, apoptosis, and others. Yet very few cancer-related genes affecting these processes have been identified in human cancers by classical methods to find mutated genes despite enormous efforts. I report here our success in readily isolating more than 100 candidate tumor suppressor genes from human tissue, estimated to represent roughly 20% of the total genes recoverable by this approach. Half of the genes are unknown and the other half include representatives of most known cancer processes. Because their expression is lost during cancer progression, they may be useful tumor markers for diagnosis and prognosis. Because these genes are not mutated, they provide opportunities for pharmacological intervention by inducing their reexpression.

Breast Neoplasms↗
PubMed2002

[A method for estimating penetrance of pathogenic mutations in a mitochondrial genome].

Variation in the manifestation age is typical of many mitochondrial diseases. The estimation of penetrance of pathogenic mutations causing such diseases is usually conducted on samples of individuals whose age exceeds the maximum age of the disease manifestation. In the case of rare diseases, samples of sufficient size sometimes cannot be formed. In this study, we propose a method for estimating penetrance involving individuals of any age. The efficiency of the method is demonstrated using Leber hereditary optic neuropathy as an example. It is shown that the method provides an unbiased estimate of penetrance and considerably reduces the error of this estimate in comparison with a sample including individuals whose age exceeds the maximum age of disease manifestation.

Age Factors↗
PubMed1991

Neurological disorders due to mutations of the mitochondrial genome.

The rapidly expanding list of human diseases due to lesions of mitochondrial DNA includes myopathies, encephalopathies, cardiomyopathies, or various combinations of the latter, leading to multisystem disorders, which can also affect visceral organs. Five maternally inherited diseases, mainly affecting muscle and brain, are due to point mutations of mitochondrial genes encoding either respiratory chain polypeptides or transfer RNAs. On the other hand, three sporadic entities, Chronic Progressive External Ophthalmoplegia, Kearns-Sayre syndrome, and Pearson's pancreas-bone marrow syndrome, are due to single large-scale deletions of mitochondrial DNA. In addition, multiple deletions are the molecular hallmark of familial encephalomyopathies, inherited as either autosomal dominant or autosomal recessive traits. Finally, tissue-specific depletion of mitochondrial DNA was found in an autosomal recessive disease affecting either muscle, liver, kidney, or a combination of the three. Point mutations and slipped mispairing during, or impairment of, mitochondrial replication are likely mechanisms involved in the pathogenesis of these lesions.

DNA, Mitochondrial↗
PubMed2026

MET Exon 14 Skipping Mutation in NSCLC: From Genomic Discovery to Biomarker-Guided Therapeutic Innovation.

INTRODUCTION: Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, and the MET exon 14 skipping mutation is a key oncogenic driver, which promotes tumor progression and provides a new direction for precision therapy. METHODS: A systematic search of English-language literature and clinical trial data related to the MET exon 14 skipping mutation from 2020-2025 was performed to summarize the role of the mutation and therapeutic advances. RESULTS: DNA-based next-generation sequencing (NGS), RNA-based NGS, and RT-qPCR were employed as the main detection methods. Preclinical models confirmed that mutations promote tumor progression by activating the RAS/MAPK pathway. Clinical trials have reported objective remission rates (ORR) of 46-68% for first-line treatment with MET inhibitors in NSCLC patients harboring MET exon 14 skipping mutations. DISCUSSION: MET exon 14 skipping mutation as a therapeutic target for NSCLC has made significant progress, and MET inhibitors are more advantageous than chemotherapy and immunotherapy, and have been recommended by national and international guidelines as a first-line treatment option. Additionally, NGS technology has the potential to dynamically monitor tumor evolution and drugresistant mutations, thereby helping to realize precision medicine. CONCLUSION: The MET exon 14 skipping mutation is an important target for the precision treatment of NSCLC, and MET-TKIs have remarkable efficacy but a prominent problem with drug resistance. The construction of a precision medicine system encompassing diagnosis, treatment, and drug resistance management through multi-omics research, technological innovation, and international collaboration is a key direction for improving prognosis.

Humans↗
PubMed2002

Isochores, GC3 and mutation biases in the human genome.

In this work we re-examined the hypothesis that the variation in GC content in the human genome is due to different regional mutational biases. For this purpose we inferred the mutational pattern by using mutation databases that are available for many genes associated with human genetic diseases. The assumption of this approach is that such mutations reflect the actual frequency distribution of mutations as they arise in the population. Four classes of genes, classified according to their GC(3) level, were included in this study: GC(3)-poor genes (GC(3)<45%), genes with intermediate GC(3) content (45% 75%). Our results show that most genes are under AT mutational biases, with very little variation compared to the expectations of neutral GC level. It is noteworthy that the mutational patterns in the GC(3)-rich genes do not appear to account for their GC(3)-richness. Instead, GC(3)-rich and very GC(3)-rich genes exhibit patterns of mutations that yield expectations of neutral GC(3) content that are much lower than their actual GC(3).

Base Composition↗
PubMed1994

Preferential replication of defective turnip yellow mosaic virus RNAs that express the 150-kDa protein in cis.

The turnip yellow mosaic virus genome encodes two proteins (the 150-kDa and 70-kDa proteins) that are proteolytically released from a single precursor and which are essential for RNA replication. Genomes with mutations in either of these coding regions were defective for independent replication in turnip protoplasts. The replication in trans of genomes with mutations in each region was studied by coinoculation with either a helper genome that carries a deletion in the coat protein gene, or with a second defective RNA that carries a mutation in the region encoding the other essential protein. Inefficient trans-replication of the defective RNAs was observed in most cases. In contrast, a defective RNA with a large deletion in the 70-kDa protein coding region could be replicated efficiently in trans, demonstrating that the cis-preference of replication can be overcome in some cases. Defective RNAs encoding wild type 150-kDa protein and defective 70-kDa protein were more efficiently replicated in trans than those encoding defective 150-kDa protein and wild type 70-kDa protein. The results suggest a model in which the 150-kDa and 70-kDa proteins form a relatively stable complex in cis on the viral RNA template.

Amino Acid Sequence↗
PubMed2026

Comprehensive genomic profiling and tumor mutational burden in parathyroid carcinoma: a nationwide real-world study from Japan.

PURPOSE: Parathyroid carcinoma (PC) is an extremely rare endocrine malignancy with limited treatment options for unresectable or recurrent cases. With the increasing use of comprehensive genomic profiling (CGP), treatment based on genomic findings is becoming more common. However, the frequency and clinical significance of elevated tumor mutational burden (TMB) in PC remain unclear because previous studies have been limited by small sample sizes. METHODS: We retrospectively analyzed genomic and clinical data of patients with PC registered in the Center for Cancer Genomics and Advanced Therapeutics database in Japan between June 2019 and March 2025. TMB values were obtained as reported by each CGP assay. TMB-H was defined as TMB&#x2009;&#x2265;&#x2009;10 mut/Mb for descriptive analyses. We also assessed genomic alterations, microsatellite instability (MSI) status, and clinicogenomic characteristics. RESULTS: Twenty-five patients with PC were included. The median assay-reported TMB was 4.0 mut/Mb (range, 0-35). Seven tumors (28.0%) had assay-reported TMB values of &#x2265;&#x2009;10 mut/Mb, including three (12.0%) with TMB&#x2009;&#x2265;&#x2009;20 mut/Mb. The most frequently altered genes were CDC73 (40%), TP53 (32%), and MEN1 (24%). No co-alterations were observed between CDC73 and MEN1 or between CDC73 and TP53. One tumor was MSI-high and was included in the TMB-H group. POLE alterations were detected in three cases, including two tumors in the TMB-H group. CONCLUSION: This nationwide, real-world study demonstrated that a subset of PCs showed elevated assay-reported TMB values and genomic features potentially related to abnormalities in DNA replication or repair pathways. These findings support the clinical relevance of comprehensive genomic profiling in identifying the molecular heterogeneity and potential therapeutic opportunities for this rare malignancy.

Humans↗
PubMed1992

Mutational risks in females: genomic imprinting and maternal molecules.

Genetic mechanisms for selective mutagenesis in female mammals might include alterations of genomic imprinting, maternally derived molecules, mitochondrial DNA or sex chromosome loci. None of these mechanisms provides an obvious explanation for the higher mutational rates observed for certain mutagens in mouse female pronuclei, but the association of DNA methylation with maternal genomic imprinting is an enticing avenue for research. Further characterization of the extent and homology of genomic imprinting among mammals is required before its relevance to mutagenesis can be determined. The existence of maternal effect mutations in mammals merits evaluation but is not yet proven. The relevance of mitochondrial DNA to female-specific mutagenesis will be greatest in multi-generational studies.

Animals↗