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PubMedDate not supplied

[Prognostic significance of additional chromosomal abnormalities in Ph positive bone marrow cells in chronic myeloid leukemia].

We studied the prognostic significance of combination of different chromosomal abnormalities and genomic mutations in Ph+ chronic myeloid leukemia patients. In general 49 cytogenetic analyses of bone marrow aspirate from 35 patients (11 of these observed in dynamics) have been carried out. The additional chromosome changes were found in 25.07% cases and approximately 80% of anomalies appeared in the blast phase. Among the secondary chromosomal abnormalities extra Ph-chromosome appeared mostly in different combinations with trisomy of chromosomes 8 and 19. Appearance of clonal differences of cells, high rate of genome mutations and of microchromosomes had negative prognostic significance on disease proceeding.

Bone Marrow Cells↗

PubMed2003

Identification of the E9/E2C cDNA and functional characterization of the gene product reveal a new repressor of transcription and replication in cottontail rabbit papillomavirus.

Cottontail rabbit papillomavirus (CRPV) genomes mutated in the trans-activation domain of the E2 protein, which stimulates both viral DNA replication and transcription, are severely impaired in their ability to induce tumors in New Zealand White rabbits. A number of papillomaviruses encode, in addition to full-length E2, a shortened E2 protein or an E2 protein fused to a short stretch of amino acids derived from the small E8 open reading frame that counteract the activities of E2. We identified and cloned the novel cDNA E9/E2C of CRPV from papillomas of New Zealand White and cottontail rabbits and characterized the functions of the encoded gene product. E9/E2C was shown to be a bona fide repressor of minimal viral promoters, with the E9 domain being essential for this activity, and to repress E1/E2-dependent replication of a CRPV origin construct. In addition, E9/E2C counteracted the transactivation effect of the full-length E2 on minimal promoters containing several E2 binding sites. To investigate the role of E9/E2C in tumorigenesis, we constructed two CRPV genomes mutated in E9/E2C. One, designated CRPV-E9atgmut-pLAII, contained a mutation in the unique start codon in the E9 open reading frame, and the second E9/E2C mutant was constructed by the introduction of a stop codon close to the splice donor site at nucleotide 3714 that additionally prevented the correct splicing of the transcript. When we infected New Zealand White rabbits with these constructs, we surprisingly noted no differences in tumor induction efficiency, viral genome copy number, and viral transcription in comparison to wild-type CRPV.

Animals↗

PubMedDate not supplied

[Biological effects in natural populations of small rodents in radiation contaminated areas. The frequency of bone marrow polyploid cells of bank voles in different years following Chernobyl accident].

On the basis of the metaphase analysis results, the peculiarities of dynamics of the genome mutation frequency (polyploid cells) were studied in bone marrow of bank voles inhabiting the areas with different radiocontamination level due to the Chernobyl accident (8-1526 kBq/m2 for 137Cs) in 1986-1991. Unexpectedly high frequencies of polypoid cells exceeding the pre-accidental level by a factor of 10(1)-10(3) were recorded in all populations studied. Relationship between the frequency of the parameter studied and the concentration of radionuclides incorporated in animal carcasses was proved. A statistically significant rise in the frequency of genome mutations with the time was revealed up to 1991, i.e. approximately to 12th post-accidental animal generation.

Animals↗

PubMed1994

A practical approach to the detection of androgen receptor gene mutations and pedigree analysis in families with x-linked androgen insensitivity.

Androgen insensitivity syndrome (AIS) is an X-linked disorder in which defects in the androgen receptor gene have prevented the normal development of both internal and external male structures in 46,XY individuals. This survey reports the analysis of 11 AIS subjects. The androgen receptor gene of these subjects was analyzed using polymerase chain reaction (PCR)-single-strand conformation polymorphism analysis and sequencing or sequencing of PCR-amplified androgen receptor gene fragments alone. In total, 10 single base changes and one partial gene deletion were detected. Seven single base changes resulted in an amino acid change, one resulted in the introduction of a premature stop codon, one event represented a single base insertion resulting in a frame-shift, and one single base change affected a donor splice site. The androgen receptor protein in genital skin fibroblasts from several patients was studied with respect to molecular mass after immunoprecipitation and SDS-PAGE. Two patients expressed a truncated receptor protein in agreement with the established genomic mutation. Pedigree analysis was performed to identify possible carriers for the syndrome in families of AIS patients using single-strand conformation polymorphism and restriction site analysis of PCR products. In one case, the polymorphic (CAG)n(CAA) repeat in exon 1 encoding a polyglutamine stretch was used to identify the mutant allele in a family with X-linked partial androgen insensitivity before the identification of the actual genomic mutation. PCR-single-strand conformation polymorphism analysis proved to be a fast and reliable technique to screen for androgen receptor gene mutations and to study the androgen receptor gene of family members of AIS-affected individuals.

Base Sequence↗

PubMedDate not supplied

Utilization of the specific-locus assay in the ad-3 region of two-component heterokaryons of Neurospora for risk assessment of environmental chemicals.

The utilization of the specific-locus assay in the ad-3 region of two-component heterokaryons of Neurospora crassa is compared with that of other eukaryotic assay systems for the evaluation of the mutagenic effects of environmental chemicals. In contrast to other in vitro specific-locus assays, the Neurospora assay can detect mutations not only at the ad-3A and ad-3B loci but also recessive lethal mutations elsewhere in the genome. Mutational damage in this system can be characterized readily by means of classical genetic techniques involving heterokaryon tests to determine genotype, and allelic complementation among ad-3BR mutations. The percentages of ad-3BR mutations showing allelic complementation with polarized or nonpolarized complementation patterns provide a presumptive identification of the genetic alterations at the molecular level in individual mutants. Dikaryon and trikaryon tests (using 3 strains carrying multilocus deletion mutations as tester strains) distinguish ad-3 mutations resulting from gene/point mutation, multilocus deletion mutation, and various types of multiple-locus mutation. The array of ad-3 mutations recovered from forward-mutation experiments can be expressed in terms of Mutational Spectra, which make it possible to make comparisons of mutational types between different doses of the same mutagen, different mutagens, or the effects of the same mutagen on different strains. Another important feature of this specific-locus assay system is that the effects of mutagens can be studied in both DNA excision repair-proficient (H-12) and -deficient (H-59) two-component heterokaryons to evaluate both quantitative and qualitative differences between the spectra of induced ad-3 mutations. The utilization of this assay on large numbers of environmental chemicals has shown that some chemicals produce predominantly, or exclusively, gene/point mutations, whereas other agents produce both gene/point mutations and multilocus deletion mutations in H-12. When the mutagenic effects of the same chemicals were compared in H-12 and H-59, marked differences between forward-mutation frequencies and Mutational Spectra of ad-3 mutations were detected.

Carcinogens↗

PubMed1998

Human Prop-1: cloning, mapping, genomic structure. Mutations in familial combined pituitary hormone deficiency.

Prop-1 is a newly isolated pituitary-specific paired-like homeodomain transcription factor whose cDNA sequence is well known in mouse. To study its involvement in human combined pituitary hormone deficiency (CPHD), we have isolated the human cDNA ortholog and determined the exon/intron organization and chromosomal localization of the human gene. A Prop-1 defect was characterized in three CPHD families. One missense mutation (R73C) involves a residue conserved in 95% of the more than 400 homeodomain proteins so far identified; in vitro splicing assays demonstrated the functional importance of the second defect, whereas the remaining mutation is a frameshift. Given the disease phenotype documented in the patients, these data, which will facilitate molecular investigations in other patients, demonstrate the crucial role of Prop-1 in the proper development of somatotrophs, lactotrophs, thyreotrophs and gonadotrophs.

Amino Acid Sequence↗

PubMed1997

Genomic and mutational analysis of the mitochondrial trifunctional protein beta-subunit (HADHB) gene in patients with trifunctional protein deficiency.

Mitochondrial trifunctional protein (TP), an enzyme of beta-oxidation, is a multienzyme complex composed of four molecules of the alpha-subunit (HADHA) containing the enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase domains and four molecules of the beta-subunit (HADHB) containing the 3-ketoacyl-CoA thiolase domain. An inborn error of this enzyme complex can cause sudden infant death syndrome, acute hepatic encephalopathy or liver failure, skeletal myopathy, or hypertrophic cardiomyopathy. TP deficiency is classified into two different biochemical phenotypes: one represents the existence of both subunits and the lack of only the 3-hydroxyacyl-CoA dehydrogenase activity and the other represents the absence of both subunits and the lack of all three TP activities, although their clinical features are similar. We have identified two Japanese patients with this disorder. Three enzyme activities of TP were undetectable in fibroblasts from these two patients. We detected two mutations in the HADHB gene from two Japanese patients, an exonic single T insertion which created a new cryptic 5' splice site and a G1331A transition (R411 K). Patient 1 was a compound heterozygote, while patient 2 was a homozygote of a G1331A transition.

Animals↗

PubMed1993

In vivo selection of randomly mutated retroviral genomes.

Darwinian evolution, that is the outgrowth of the fittest variants in a population, usually applies to living organisms over long periods of time. Recently, in vitro selection/amplification techniques have been developed that allow for the rapid evolution of functionally active nucleic acids from a pool of randomized sequences. We now describe a modification of the nucleic acid-evolution protocol in which selection and amplification take place inside living cells by means of a retroviral-based replication system. We have generated a library of HIV-1 DNA genomes with random sequences in particular domains of the TAR element, which is the binding site for the Tat trans-activator protein. This mixture of HIV genomes was transfected into T cells and outgrowth of the fittest viruses was observed within two weeks of viral replication. The results of this in vivo selection analysis are consistent with the notion that primary sequence elements in both TAR bulge and loop domains are critical for Tat-mediated trans-activation and viral replication.

Base Sequence↗

PubMedDate not supplied

Molecular, immunological and clinical properties of mutated hepatitis B viruses.

Hepatitis B virus (HBV) is at the origin of severe liver diseases like chronic active hepatitis, liver cirrhosis and hepatocellular carcinoma. There are some groups of patients with high risk of generation of HBV mutants: infected infants, immunosuppressed individuals (including hemodialysis patients), patients treated with interferon and lamivudine for chronic HBV infection. These groups are the target for molecular investigations reviewed in this paper. The emergence of lamivudine- or other antiviral-resistant variants, rises concern regarding long term use of these drugs. Infection or immunization with one HBV subtype confers immunity to all subtypes. However, reinfection or reactivation of latent HBV infection with HBV mutants have been reported in patients undergoing transplant and those infected with HIV. Mutations of the viral genome which are not replicative incompetent can be selected in further course of infection or under prolonged antiviral treatment and might maintain the liver disease. Four open reading frames (ORF) which are called S-gene, C-gene, X-gene and P-gene were identified within the HBV genome. Mutations may affect each of the ORFs. Mutated S-genes were described to be responsible for HBV-infections in successfully vaccinated persons, mutated C-genes were found to provoke severe chronic liver diseases, mutated X-genes could cause serious medical problems in blood donors by escaping the conventional test systems and mutated P-genes were considered to be the reason for chemotherapeutic drug resistance. This paper reviews molecular, immunological and clinical aspects of the HBV mutants.

Animals↗

PubMed1988

Deletions of mitochondrial DNA in Kearns-Sayre syndrome.

We have identified large-scale deletions in muscle mitochondrial DNA (mtDNA) in seven of seven patients with Kearns-Sayre syndrome (KSS). We found no detectable deletions in the mtDNA of ten non-KSS patients with other mitochondrial myopathies or encephalomyopathies, or three normal controls. The deletions ranged in size from 2.0 to 7.0 kb, and did not localize to any single region of the mitochondrial genome. The proportion of mutated genomes in each KSS patient ranged from 45% to 75% of total mtDNA. There was no correlation between the size or site of the deletion, biochemical abnormality of mitochondrial enzymes, or clinical severity. The data bolster arguments that KSS is a unique disorder and genetic in origin.

Adolescent↗

PubMed2026

Identification of ultrasound-associated gene candidates in myeloid cells and construction of a prognostic risk model for acute myeloid leukemia.

BACKGROUND: Incorporating ultrasound (US) treatment sensitivity analysis may improve the treatment of acute myeloid leukemia (AML). METHODS: This study integrated single-cell and bulk datasets for analysis. Differential expression analysis between US-treated and control samples was performed using limma package. The AUCell package was used to calculate US-associated scores in the single-cell dataset. Differentially expressed genes (DEGs) between the specific groups were identified, followed by intersection analysis with previously identified DEGs. Univariate regression, Least Absolute Shrinkage and Selection Operator (LASSO) analysis (using the glmnet package), and stepwise multivariate regression (using the MASS package) were used to refine the candidate genes and to construct a risk model. The model genes were validated using in vitro experiments. Enrichment analysis was conducted using gene set enrichment analysis (GSEA), and immune infiltration was evaluate by single-sample GSEA (ssGSEA) and ESTIMATE algorithms. The correlations between RiskScores and drug sensitivity were analyzed by oncoPredict package. Finally, tumor mutational burden (TMB) and genomic mutations were compared between the risk groups. RESULTS: Nine prognostic signatures (SPINK2, HNRNPAB, SH3BGRL3, CLEC11A, ITGA4, RPL39L, MX1, HEXIM1, and MAP4K4) were identified. Particularly, low expression of SPINK2 attenuated the activity and invasion of AML cells. High-risk group had higher immune cell infiltration. Eight drugs were predicted to be correlated with the RiskScore model. DNMT3A and RUNX1 showed higher mutation frequencies in the high-risk group, whereas KIT and MUC16 showed higher mutation frequencies in the low-risk group. CONCLUSION: The RiskScore model established in this study provides a theoretical basis for clinically screening responsive populations and optimizing treatment strategies.

Humans↗

PubMed2006

An unusual pattern of spontaneous mutations recovered in the halophilic archaeon Haloferax volcanii.

Spontaneous mutations in the orotate:phosphoribosyl transferase (pyrE2) gene of the halophilic archaeon Haloferax volcanii were selected by 5-fluoroorotic acid plus uracil at a rate of approximately 2 x 10(-8)/cell division in fluctuation and null-fraction tests but approximately 6 x 10(-8)/cell division in mutation-accumulation tests. The corresponding genomic mutation rates were substantially lower than those observed for other mesophilic microbial DNA genomes on the basis of similar target genes. The mutational spectrum was dominated by indels adding or deleting multiples of 3 bp. Properties of the organism contributing to this unusual mutational pattern may include phenotypic lag caused by a high chromosomal copy number and efficient promotion of strand misalignments by short direct repeats.

Genes, Archaeal↗

PubMed2002

[GeneChip system from a bioinformatical point of view].

GeneChip (Affymetrix, Inc., USA) employs a specific method for spotting DNA probes on chips, which is different from any other DNA chips, and can complete the whole process from sample preparation to data construction and analysis. The GeneChip system can be applied to both gene expression analysis and genomic mutation analysis, which would play an important role in human genome analysis in the future. Techniques for data construction ("wet" experimental techniques), which are the major components in the GeneChip system, are generally established as routine work in the first screening process in most laboratories worldwide. The most important point would be how we exchange experimental data produced by researchers and gene/genome information available both on the public and the commercial bases so that we reduce useful information on gene expression. Recently, the center of the research has been shifting to computing technology for data processing ("bioinformatics"). This article separately deals with gene expression analysis and genomic analysis, with emphasis on bioinformatics. We describe the data on gene expression screening, the gene targeting process, the analysis of genomic DNA mutations using the P53 probe array, and the HuSNP mapping assays, by presenting our experimental examples.

Computational Biology↗

PubMed1994

Somatic mosaicism for a newly identified splice-site mutation in a patient with adenosine deaminase-deficient immunodeficiency and spontaneous clinical recovery.

Absent or severely reduced adenosine deaminase (ADA) activity produces inherited immunodeficiency of varying severity, with defects of both cellular and humoral immunity. We report somatic mosaicism as the basis for a delayed presentation and unusual course of a currently healthy young adult receiving no therapy. He was diagnosed at age 2 1/2 years because of life-threatening pneumonia, recurrent infections, failure of normal growth, and lymphopenia, but he retained significant cellular immune function. A fibroblast cell line and a B cell line, established at diagnosis, lacked ADA activity and were heteroallelic for splice-donor-site mutation in IVS 1 (+1GT-->CT) and a missense mutation (Arg101Gln). All clones (17/17) isolated from the B cell mRNA carried the missense mutation, indicating that the allele with the splice-site mutation produced unstable mRNA. In striking contrast, a B cell line established at age 16 years expressed 50% of normal ADA; 50% of ADA mRNA had normal sequence, and 50% had the missense mutation. Genomic DNA contained the missense mutation but not the splice-site mutation. All three cell lines were identical for multiple polymorphic markers and the presence of a Y chromosome. In vivo somatic mosaicism was demonstrated in genomic DNA from peripheral blood cells obtained at 16 years of age, in that less than half the DNA carried the splice-site mutation (P < .002, vs. original B cell line). Consistent with mosaicism, erythrocyte content of the toxic metabolite deoxyATP was only minimally elevated. Somatic mosaicism could have arisen either by somatic mutation or by reversion at the site of mutation. Selection in vivo for ADA normal hematopoietic cells may have played a role in the return to normal health, in the absence of therapy.

Adenosine Deaminase↗

PubMed1993

Wilms tumor genes.

Multiple 'WT' genes exist. The WT1 gene at chromosomal band 11p13 has been cloned and is known to be important in the etiology of at least some tumors by virtue of the identification of both germline and somatic mutations in WT patients. Genes at 11p15 and 16q are also involved, either as initiating or tumor progression events. An unlocalized familial predisposition gene is also known to be important etiologically. The identification of several genes that are involved in the etiology or progression of WT, the preferential loss of maternally derived alleles in tumor tissue, and the observed reduction to 11p homozygosity in normal tissue DNA from some patients, all strikingly indicate that a simple, one-locus-'two-hit' genetic model for WT is inadequate. The question is not if this model needs to be modified, but how it should be modified, or if it is even valid enough to be a starting point for understanding the genetics of Wilms tumor. To begin to address this, several questions can be asked. Do all Wilms tumors carry mutations at the WT1 locus? Do both alleles at the WT1 locus need to be inactivated or lost for tumorigenesis? Or, instead, do some WT1 mutations act dominantly? Do patients with bilateral disease carry germline mutations as originally hypothesized, or, as more recently suggested, is bilateral disease the result of early somatic mutations, genomic imprinting, or multifactorial inheritance? Must mutations at an 11p15 locus and/or 11p15 LOH accompany WT1 mutations, or do 11p13 and 11p15 mutations act independently of each other? Have tumors from familial WT cases (who do not carry germline WT1 mutations) sustained somatic mutations at the WT1 locus, the 11p15 locus or the 16q locus? Conversely, do tumors from sporadic WT patients carry somatic mutations at the non-11p familial predisposition gene? Will most tumors be found to carry mutations at the same one or two loci, but differ only with regard to whether the mutations are somatic or germline? Are effects of genomic imprinting layered over, so to speak, a framework of classically mendelian mutations, or in some cases is imprinting the mechanism by which genes are inactivated or their normal function modulated? Although not definitive, there are data that bear on some of these questions. Germline mutations have been observed in patients with bilateral tumors, but may not prove to be a universal feature of bilateral disease.(ABSTRACT TRUNCATED AT 400 WORDS)

Genes, Wilms Tumor↗

PubMed2000

Unequal expression of allelic kainate receptor GluR7 mRNAs in human brains.

We describe here the first example of an exonic polymorphism that affects the primary structure of a human ionotropic glutamate receptor. The human kainate receptor GluR7 gene contains a thymine (T)/guanine (G) nucleotide variation that determines a serine or alanine at position 310 in the extracellular region of GluR7 receptor subunits. Our finding contrasts with a previous report that suggested that GluR7 transcripts were RNA-edited at this site. Whole-cell patch-clamp recordings did not detect differences in receptor activation and desensitization between the human GluR7 receptor isoforms expressed in HEK-293 cells. Analysis of 41 tissue samples obtained from 30 human brains revealed expression level differences between GluR7 alleles expressed in the same brain. The expression level of the allelic GluR7 mRNAs differed in 27 samples from 1.2- to 12.7-fold. Unequal expression level of allelic mRNAs is characteristic for genes that are affected by genomic imprinting or that contain mutations. Genomic imprinting in most cases is conserved between human and mice. However, we did not detect unequal expression of allelic GluR7 mRNAs in mice. Our results are important for future studies that explore a potential role or roles for GluR7 receptors in the brain and for neurological disorders.

Alleles↗

PubMed1998

Apoptotic repair of genotoxic tissue damage and the role of p53 gene.

The spontaneous mutation rate per replication per genome is nearly invariant in microbes; however, the rate of spontaneous genomic mutations in higher eukaryotes is much higher. Furthermore, the mutation rates per locus per generation among Drosophila, mice and humans are similar, despite the large differences in generation time. A simple explanation for these findings is that mice and humans have a specific antimutagenic mechanism that is lacking in Drosophila. I propose that apoptotic repair-deletion of genotoxic damage-bearing cells-operates in mammalian germ cells and that it works more accurately in humans than in mice because of a slower rate of cell turnover and a longer generation time. It has been a long-standing puzzle that germline mutation frequencies decrease markedly as the dose-rate of radiation is lowered in mice but not in Drosophila. This can be readily explained by p53-dependent apoptotic repair, because the p53 gene is absent from the genome of Drosophila. Fetuses of p53+/+ mice have proficient apoptotic repair capacity for X-ray-induced teratogenic damage, but p53-null fetuses completely lack this capacity. Further, I propose that the primary role of the p53 gene is to guard germ cells and embryos from genotoxic damage. This implies that the tumour suppressor function of the p53 gene results from p53-dependent apoptotic deletion of cells with genotoxic damage. The reasoning behind this proposal is given by reviewing reports that Drosophila larvae are insensitive to tumour formation after irradiation. Finally, I discuss the genetic effects of radiation in humans.

Animals↗

PubMed2004

Microarray gene expression profiling of B-cell chronic lymphocytic leukemia subgroups defined by genomic aberrations and VH mutation status.

PURPOSE: Genomic aberrations and mutational status of the immunoglobulin variable heavy chain (VH) gene have been shown to be among the most important predictors for outcome in patients with B-cell chronic lymphocytic leukemia (B-CLL). In this study, we report on differential gene expression patterns that are characteristic for genetically defined B-CLL subtypes. MATERIALS AND METHODS: One hundred genetically well-characterized B-CLL samples, together with 11 healthy control samples, were analyzed using oligonucleotide arrays, which test for the expression of some 12,000 human genes. RESULTS: Aiming at microarray-based subclassification, class predictors were constructed using sets of differentially expressed genes, which yielded in zero or low misclassification rates. Furthermore, a significant number of the differentially expressed genes clustered in chromosomal regions affected by the respective genomic losses/gains. Deletions affecting chromosome bands 11q22-q23 and 17p13 led to a reduced expression of the corresponding genes, such as ATM and p53, while trisomy 12 resulted in the upregulation of genes mapping to chromosome arm 12q. Using an unsupervised analysis algorithm, expression profiling allowed partitioning into predominantly VH-mutated versus unmutated patient groups; however, association of the expression profile with the VH mutational status could only be detected in male patients. CONCLUSION: The finding that the most significantly differentially expressed genes are located in the corresponding aberrant chromosomal regions indicates that a gene dosage effect may exert a pathogenic role in B-CLL. The significant difference in the partitioning of male and female B-CLL samples suggests that the genomic signature for the VH mutational status might be sex-related.

Adult↗