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At least 307 records · Page 17Linked to original sources
PubMed2026

Fault Lines in the Genome: Somatic DNA Mutations in Aging and Neurodegeneration.

The human genome is both fragile and resilient: prone to alteration yet protected by extensive repair mechanisms. With age, individuals accumulate genetic damage from environmental factors and cell-intrinsic processes, with effects ranging from benign nucleotide shifts to disease-driving mutations. Such alterations to the genetic code outside the germline are described as somatic mutations and display striking heterogeneity across cell types. Recently, somatic mutations have emerged as a hallmark feature of aging in the body's longest-lived tissue: the central nervous system (CNS). The distinctively long lifespan, high metabolism, electrochemical activity, and unique epigenome of CNS cells may render them especially vulnerable to mutational accumulation. The CNS therefore provides a model for understanding how somatic mutations drive cellular dysfunction beyond an established role in cancer. Here, we review the somatic mutations that arise in the brain across lifespan, the mechanisms that lead to their formation, and their potential contributions to aging and age-related disease.

Journal Article↗
PubMed2006

Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella.

Horizontal gene transfer plays a major role in microbial evolution. However, newly acquired sequences can decrease fitness unless integrated into preexisting regulatory networks. We found that the histone-like nucleoid structuring protein (H-NS) selectively silences horizontally acquired genes by targeting sequences with GC content lower than the resident genome. Mutations in hns are lethal in Salmonella unless accompanied by compensatory mutations in other regulatory loci. Thus, H-NS provides a previously unrecognized mechanism of bacterial defense against foreign DNA, enabling the acquisition of DNA from exogenous sources while avoiding detrimental consequences from unregulated expression of newly acquired genes. Characteristic GC/AT ratios of bacterial genomes may facilitate discrimination between a cell's own DNA and foreign DNA.

Bacterial Proteins↗
PubMed1989

The micronucleus test in Xenopus: a new and simple 'in vivo' technique for detection of mutagens in fresh water.

The aim of this study was to extend the micronucleus test to Xenopus laevis to screen water for potential mutagens. Up to now, the most commonly used methods for screening fresh water are the bacterial tests (Ames tests). Ames tests are well validated, but are merely in vitro bacterial assays which can only detect point mutations whereas the micronucleus test is an in vivo assay using a vertebrate species, and thus is able to detect both chromosome and genome mutations. This study was designed to optimize the micronucleus test for Xenopus. Three different variables were investigated: (i) the effect of temperature; (ii) the effect of the stage of larval development; and (iii) the effect of varying or continuous exposure concentrations. In addition, a dose-response curve was established for eight concentrations of benzo[alpha]pyrene. The results indicate that the micronucleus test with Xenopus can be used to monitor water pollution.

Animals↗
PubMed2002

Jak3 expression and genomic sequence in pediatric acute lymphoblastic leukemia.

Janus tyrosine kinase 3 (JAK3) is one of several key regulatory enzymes in B-cell precursors which is highly conserved between multiple species. The gene for Jak3 has been mapped to human chromosome 19p12-13.1 and encompasses 23 exons. Constitutively high levels of JAK3 activity may contribute to drug resistance and enhanced clonogenicity of leukemic B-cell precursors from children and infants with acute lymphoblastic leukemia (ALL). As part of a systematic effort to accurately determine the genomic sequence of Jak3 gene in normal and leukemic B-cell precursors, we sequenced a relatively short region of Jak3 spanning two introns, originally termed introns 10 and 11. This genomic sequence appeared in certain RT-PCR products from our analysis of Jak3 gene expression in pediatric, as well as infant, primary ALL cells. Unexpectedly, a gap in the original Jak3 genomic sequence was found in intron 10 across the sequence matching to an Alu element. Furthermore, the sequence obtained from intron 11 did not match at all to that previously reported, and the length of the intron was much larger than expected at 1.1 kb. Homology to Alu elements (three regions, 699 bp total) and a LINE2 element (one region, 189 bp total) were seen across the entire region covering exons 10-12 (2.1 kb total). Two potential single nucleotide polymorphisms (SNPs) were observed in intron 11. No apparent genomic mutation was found across this region in leukemic B-cell precursors from any of the ALL patients examined. This newly described sequence corrects the previous published genomic sequence from this region rather than identifying an insertion or translocation specific to these ALL cases. Our results significantly extend previous efforts to determine the genomic sequence of Jak3 and analyze its expression in childhood pro-B ALL and other forms of ALL.

B-Lymphocytes↗
PubMed1993

[ts-Mutations in the genomes of cold-adapted variants of influenza A/Hong Kong/1/68(H3N2) and A/Victoria/35/72(H3N2) viruses].

The phenotype and localization of ts mutations in genomes of the influenza A/Victoria/30-ir (A/Vic/30-ir) and A/Hong Kong/17-ir (A/HK/17-ir) cold-adapted (ca) viruses were studied. Using the recombination analysis in chick embryo fibroblasts (CEF) we determined that influenza A/HK/17-ir ca virus carries ts mutations in three "internal" genes, i.e., PB1, NP and M, and influenza A/Vic/30-ir ca virus carries ones in four genes, i.e., PA, NP, M and NS. We have revealed ts mutations for NA gene in none of these viruses. Prior to the analysis of ts mutations in HA gene of influenza A/HK/17-ir and A/Vic/30-ir ca viruses, three cloning steps were performed in chick embryos (CE) by the method of limiting dilutions at 34 degrees C followed by selection of some strains with the most prominent ts phenotype. The cloned strains with such phenotypes were shown to repeat stable results within the recombination analysis in CE, i.e., none from the cloned strains of A/HK/17-ir ca virus recombined in CE at 40 degrees C with the 46 ts mutant, while recombination of this mutant with the cloned A/Vic/30-ir ca strains led to formation of the ts progeny. Thereafter our data result in conclusion that ts mutations in the PA gene must lead to some insignificant contribution for the expression of general ts phenotype among the ca strains as far as this sign is clearly displayed by both viruses, although only one of them, i.e., A/HK/17-ir carries ts mutation in the HA gene.

Adaptation, Physiological↗
PubMed2004

Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths.

Ataxia-telangiectasia (A-T) is an autosomal recessive neurological disorder caused by mutations in the ATM gene. Classical splicing mutations (type I) delete entire exons during pre-mRNA splicing. In this report, we describe nine examples of nonclassical splicing mutations in 12 A-T patients and compare cDNA changes to estimates of splice junction strengths based on maximum entropy modeling. These mutations fall into three categories: pseudoexon insertions (type II), single nucleotide changes within the exon (type III), and intronic changes that disrupt the conserved 3' splice sequence and lead to partial exon deletion (type IV). Four patients with a previously reported type II (pseudoexon) mutation all shared a common founder haplotype. Three patients with apparent missense or silent mutations actually had type III aberrant splicing and partial deletion of an exon. Five patients had type IV mutations that could have been misinterpreted as classical splicing mutations. Instead, their mutations disrupt a splice site and use another AG splice site located nearby within the exon; they lead to partial deletions at the beginning of exons. These nonclassical splicing mutations create frameshifts that result in premature termination codons. Without screening cDNA or using accurate models of splice site strength, the consequences of these genomic mutations cannot be reliably predicted. This may lead to further misinterpretation of genotype-phenotype correlations and may subsequently impact upon gene-based therapeutic approaches.

Ataxia Telangiectasia↗
PubMed2001

Rapid mutational declines of viability in Drosophila.

High rates of mildly deleterious mutation could cause the extinction of small populations, reduce neutral genetic variation and provide an evolutionary advantage for sex. In the first attempts to estimate the rate of mildly deleterious mutation, Mukai and Ohnishi allowed spontaneous mutations to accumulate on D. melanogaster second chromosomes shielded from recombination and selection. Viability of the shielded chromosomes appeared to decline rapidly, implying a deleterious mutation rate on the order of one per zygote per generation. These results have been challenged, however; at issue is whether Mukai and Ohnishi may have confounded viability declines caused by mutation with declines resulting from environmental changes or other extraneous factors. Here, using a method not sensitive to non-mutational viability changes, I reanalyse the previous mutation-accumulation (MA) experiments, and report the results of a new one. I show that in each of four experiments, including Mukai's two experiments, viability declines due to mildly deleterious mutations were rapid. The results give no support for the view that Mukai overestimated the declines. Although there is substantial variation in estimates of genomic mutation rates from the experiments, this variation is probably due to some combination of sampling error, strain differences and differences in assay conditions, rather than to failure to distinguish mutational and non-mutational viability changes.

Animals↗
PubMed2000

mRNA mutations of type I protein kinase A regulatory subunit alpha in T lymphocytes of a subject with systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is an autoimmune disorder of indeterminate etiology characterized by multiple T lymphocyte immune effector dysfunctions. Protein kinase A (PKA) isozymes contribute to the regulation of T cell immune effector functions. In SLE T cells, there is a profound deficiency of PKA-I isozyme activity characterized by both reduced RI alpha transcript and RI alpha protein levels. To identify a molecular mechanism(s) for this isozyme deficiency, we utilized single-strand conformation polymorphism (SSCP) analysis to detect structural changes in the cDNA. Of 10 SLE subjects, cDNAs from a single subject revealed a shifted band. Sequence analyses demonstrated that a shifted SSCP band from SLE T cells carried heterogeneous transcript mutations, including deletions, transitions and transversions. Most of these transcript mutations are clustered adjacent to GAGAG motifs and CT repeats-regions that are susceptible to transcript editing and/or molecular misreading. By contrast, no genomic mutations were identified. These results suggest the occurrence of mRNA editing and/or defective function of RNA polymerase in a subject with SLE. Mutant RI alpha transcripts are pathophysiolgically significant, for they can encode diverse, aberrant RI alpha isoforms, including truncated, dominant-negative subunits, resulting in deficient PKA-I activity. We propose that deficient PKA-I isozyme activity contributes to the pathogenesis of SLE by hindering effective signal transduction and impairing T cell effector functions.

Codon↗
PubMed2004

Genomic variations in myeloperoxidase gene in the Japanese population.

Myeloperoxidase (MPO; EC 1.11.1.7) is a lysosomal hemeprotein that plays an important role in the host defense mechanism against microbial diseases. This neutrophil disorder, characterized by the lack of MPO, may result in a weakened defense activity. Complete MPO deficiency has been postulated to be to originate from genomic mutation. Recently, two Japanese patients were reported with MPO deficiency. Both had base substitutions in the exon 9 region of the MPO gene; a region in close proximity functionally important residue, His502. Genomic DNA from 387 Japanese individuals was examined to determine the prevalence of these recently discovered base substitutions. None of these DNA samples possessed the mutations found in the MPO deficient cases, though two synonymous and one non-synonymous mutation were found. The frequency of mutation in the exon 9 coding region was estimated to be one heterozygote in 129, thus the homozygote of such mutations would be revealed one in 16,000 in the Japanese population.

Genetic Variation↗
PubMed2004

Large-scale mitochondrial DNA deletion mutations and nuclear genome instability in human breast cancer.

Deletion mutations in mitochondrial (mt) DNA (mtDNA) as well as microsatellite instability (MSI) and loss of heterozygosity (LOH) in nuclear DNA (nDNA) exist in human cancer. We determined if: (1) large-scale mtDNA deletion mutations were present in cancerous and not in normal breast tissue, and (2) combining mt- and nDNA findings would provide complementary information to identify breast cancer. Thirty-nine matched breast cancer/histologically normal and 23 "true" normal tissue samples from women without breast cancer were microdissected and DNA extracted. 4977, approximately 3938, approximately 4388 and approximately 4576bp deletions were observed, with the 4576bp deletion being present in 0% of true normal, 13% of histologically normal specimens from a cancerous breast and 77% of breast cancers. The other three deletions were not specific to a breast containing cancer. LOH was found in 66.7% and MSI in 38.5% of samples. 38/39 (97.4%) tumors had at least one nDNA or 4576bp mtDNA alteration, suggesting that mt- and nDNA analysis provides complementary information in breast cancer detection. The 4576bp deletion appears to indicate cancer in the breast. The higher mtDNA copy number in cancer coupled with a mtDNA deletion mutation which appears specific for breasts which contain cancer may prove to be a good target to screen for cancer in the breast, including specimens of low and/or mixed cellularity.

Alleles↗
PubMed2026

Caloric restriction modulates genome-wide somatic mutation in mice.

Somatic mutations accumulate throughout life in every cell, and this process constitutes one of the hallmarks of aging-genomic instability. Caloric restriction (CR) has been shown to extend lifespan across diverse species. Using high-fidelity duplex DNA sequencing of bulk liver, bulk kidney, hepatocytes, and cerebellar neurons, we found that CR in mice reduces genome-wide somatic mutation burdens across multiple tissues and cell types. CR reduced both substitution and insertion/deletion burdens, with the magnitude of these effects varying across sample types. CR also decreased the activity of the enigmatic single-base substitution (SBS) mutational process SBS5 that gives rise to most mutations in mammals. Surprisingly, the mutation burden reduction from CR was greatest in transcriptionally inactive regions. This work illuminates links between diet, aging, and genomic integrity and establishes genomic integrity as a modifiable axis of aging.

DNA↗
PubMed2000

Mutations of the core promoter and response to interferon treatment in chronic replicative hepatitis B.

In chronic replicative hepatitis B the significance of mutations in the basic core promoter (BCP), core upstream regulatory sequences (CURS) and negative regulatory element (NRE) for response to interferon (IFN) is unknown. A sequence analysis of the NRE, CURS, BCP, and precore region was performed from sera of 96 patients with chronic replicative hepatitis B (64 hepatitis B e antigen [HBeAg]-positive patients and 32 HBeAg-negative patients) treated with alfa-IFN (IFN-alpha). The overall sustained response (SR) rate to IFN was 30% with no significant difference between HBeAg-positive and HBeAg-negative patients. IFN responsiveness correlated to hepatitis B virus (HBV)-DNA levels, hepatitis B surface antigen (HBsAg) levels, the number of mutations in the complete BCP, especially nucleotide (nt) region 1753 to 1766 and mutations at nt 1762 and 1764. In HBeAg-positive hepatitis, SR to IFN was associated with a high number of mutations in the BCP (P <.04) and nucleotide region 1753 to 1766 (P <.015) as well as mutations at nucleotide 1764 (P <.007). In HBeAg-negative hepatitis, SR to IFN correlated with a low number of mutations in the BCP (P <.04) and nucleotide region 1753 to 1766 (P <.02) and a wild-type sequence at nt 1764 (P <.003). Prediction of IFN response was possible on the basis of nt 1764 in 77% of HBeAg-positive patients and 78% of HBeAg-negative patients. IFN response did not correlate with the occurrence of the 1896 mutation, mutations in the CURS or NRE, disease duration, ethnic origin of the patient, alanine transaminase (ALT) levels and HBV genotype. Our data suggest that HBV genome mutations located within the BCP are determinants of a response to IFN therapy.

Adult↗
PubMed2025

Multimodal deep learning for immunotherapy response prediction and biomarker discovery in non-small cell lung cancer.

OBJECTIVE: Immunotherapy has emerged as a promising treatment for advanced non-small cell lung cancer (NSCLC), but accurately predicting which patients will benefit from it remains a major clinical challenge. To address this, we aim to develop a novel multimodal method, DeepAFM, that integrates histopathology, genomic features, and clinical information to predict patient responses to anti-PD-(L)1 immunotherapy. MATERIALS AND METHODS: A total of 93 patients with advanced NSCLC were included in this study. Histopathological whole-slide images were processed using a self-supervised VQVAE2 for representation learning. PCA and K-means clustering were then applied for dimensionality reduction and feature grouping. Key regions of interest were visualized through permutation importance evaluation and color-coding techniques. The extracted histopathological features, along with genomic alterations and clinical variables, were integrated into the DeepAFM multimodal prediction model. RESULTS: The DeepAFM achieved a high predictive performance with an area under the curve (AUC) of 0.77 (95% confidence interval: 0.69-1.00). Attention-based heatmaps revealed that the model could identify critical pathological patterns, genomic mutations, and clinical indicators associated with patient responses to immunotherapy. DISCUSSION: The integration of multimodal data enabled the model to capture complex interactions among pathology, genomics, and clinical characteristics, enhancing the interpretability and predictive power of immunotherapy response prediction. The visualization techniques facilitated the identification of biologically meaningful features and potential biomarkers. CONCLUSION: This study demonstrates the effectiveness of the DeepAFM in predicting responses to immunotherapy in advanced NSCLC. The approach not only improves prediction accuracy but also provides valuable insights for personalized treatment strategies and biomarker discovery.

Humans↗
PubMed1993

A general model of carcinogenesis (I)--Tumor evolution and gene deletion.

Carcinogenesis is functionally a deletion alteration rather than addition of genetic information. Repressor genes may be more sensitive to 'neutral' mutations of DNA than those of structural genes, since selection pressure for deletion of repressors is extremely low in multicellular organisms. Dysfunction of repressors caused by genomic mutation induces autonomic expression of structural genes which is programmed a priori in each cell. Tumor progression can be explained by this deletion model with abnormal DNA repair. Alteration of DNA repairing units may be the initial mutation in carcinogenesis.

Animals↗
PubMed2004

The challenge of documenting mutation across the genome: the human genome variation society approach.

New methods for the detection of mutations and the completion of the human genome sequencing project have contributed to an exponential rise in variation information that must be collected, quality controlled, documented, and stored safely to ensure future availability to health care professionals, researchers, and others. There may be anywhere from one to more than 1,000 mutations in any given gene. To date, this information has been collected by general databases such as Online Mendelian Inheritance in Man (OMIM) or the Human Gene Mutation Database (HGMD), which collect only published mutations and, in the case of OMIM, selected published mutations. Unpublished mutations have made their way into Locus Specific Databases (LSDBs), and these can often contain as many unpublished mutations as published ones, in addition to other more detailed gene-specific information. LSDBs, however, do not exist for all genes at this time. Through their interactions, a number of members of the Human Genome Variation Society (HGVS) have developed nomenclature, standard software to curate mutations in gene specific databases, a WayStation to collect and review new mutations from research and diagnostic laboratories, and central databases to store and display these mutations and their associated phenotypes. Nomenclature is now well defined for the commonest types of mutation, with work continuing on systematically naming the more complex types. Other projects, such as dedicated specialized software for LSDBs, are in the early stages of development.

Computational Biology↗
PubMed1993

A histidine protein kinase is involved in polar organelle development in Caulobacter crescentus.

Mutations having pleiotropic effects on polar organelle development (pod) in Caulobacter crescentus have been identified and shown to occur in at least 13 genes scattered throughout the genome. Mutations at each locus affect a unique combination of polar traits, suggesting that complex interactions occur among these genes. The DNA sequence of one of these genes, pleC, indicates that it is homologous to members of the family of histidine protein kinase genes. Membes of this family include the senor components of the bacterial two-component regulatory systems. Furthermore, in vitro experiments demonstrated that the PleC protein was capable of autophosphorylation. These results suggest that the PleC protein (and perhaps the proteins encoded by the other pod genes as well) regulates the expression of genes involved in polar organelle development through the phosphorylation of key regulatory proteins. The use of a phosphorelay system cued to internal changes in the cell would provide a mechanism for coordinating major changes in gene expression with the completion of specific cell cycle events.

Amino Acid Sequence↗
PubMed1993

A mutation within intron 3 of the Pax-3 gene produces aberrantly spliced mRNA transcripts in the splotch (Sp) mouse mutant.

The splotch (Sp) mouse mutant displays defects in neural tube closure in the form of exencephaly and spina bifida. Recently, mutations in the Pax-3 gene have been described in the radiation-induced Spr and Sp2H alleles. This led us to examine the integrity of the Pax-3 gene and its cellular mRNA transcript in the original, spontaneously arising Sp allele. A complex mutation in the Pax-3 gene including an A-->T transversion at the invariant 3' AG splice acceptor of intron 3 was identified in the Sp/Sp mutant. This genomic mutation abrogates the normal splicing of intron 3, resulting in the generation of four aberrantly spliced mRNA transcripts. Two of these Pax-3 transcripts make use of cryptic 3' splice sites within the downstream exon, generating small deletions which disrupt the reading frame of the transcripts. A third aberrant splicing event results in the deletion of exon 4, while a fourth retains intron 3. These aberrantly spliced mRNA transcripts are not expected to result in functional Pax-3 proteins and are thus responsible for the phenotype observed in the Sp mouse mutant.

Alternative Splicing↗
PubMed1996

Muller's ratchet decreases fitness of a DNA-based microbe.

Muller proposed that an asexual organism will inevitably accumulate deleterious mutations, resulting in an increase of the mutational load and an inexorable, ratchet-like, loss of the least mutated class [Muller, H.J. (1964) Mutat. Res. 1, 2-9]. The operation of Muller's ratchet on real populations has been experimentally demonstrated only in RNA viruses. However, these cases are exceptional in that the mutation rates of the RNA viruses are extremely high. We have examined whether Muller's ratchet operates in Salmonella typhimurium, a DNA-based organism with a more typical genomic mutation rate. Cells were grown asexually under conditions expected to result in high genetic drift, and the increase in mutational load was determined. S. typhimurium accumulated mutations under these conditions such that after 1700 generations, 1% of the 444 lineages tested had suffered an obvious loss of fitness, as determined by decreased growth rate. These results suggest that in the absence of sex and with high genetic drift, genetic mechanisms, such as back or compensatory mutations, cannot compensate for the accumulation of deleterious mutations. In addition, we measured the appearance of auxotrophs, which allowed us to calculate an average spontaneous mutation rate of approximately 0.3-1.5 x 10(-9) mutations per base pair per generation. This rate is measured for the largest genetic target studied so far, a collection of about 200 genes.

Adenine↗