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At least 721 records · Page 40Linked to original sources
PubMed2003

Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes.

Hypermethylation of multiple CpG islands is a common event in cancer. To assess the prognostic values of this epigenetic alteration, we developed Methylation Target Array (MTA), derived from the concept of tissue microarray, for simultaneous analysis of DNA hypermethylation in hundreds of tissue genomes. In MTA, linker-ligated CpG island fragments were digested with methylation-sensitive endonucleases and amplified with flanking primers. A panel of 468 MTA amplicons, which represented the whole repertoire of methylated CpG islands in 93 breast tumors, 20 normal breast tissues, and 4 breast cancer cell lines, were arrayed on nylon membrane for probe hybridization. Positive hybridization signals detected in tumor amplicons, but not in normal amplicons, were indicative of aberrant hypermethylation in tumor samples. This is attributed to aberrant sites that were protected from methylation-sensitive restriction and were amplified by PCR in tumor samples, while the same sites were restricted and could not be amplified in normal samples. Hypermethylation frequencies of the 10 genes tested in breast tumors and cancer cell lines were 60% for GPC3, 58% for RASSF1A, 32% for 3OST3B, 30% for HOXA5, 28% for uPA, 25% for WT1, 23% for BRCA1, 9% for DAPK1, and 0% for KL. Furthermore, hypermethylation of 5 to 7 loci of these genes was significantly correlated with hormone receptor status, clinical stages, and ages at diagnosis of the patients analyzed. This novel approach thus provides an additional avenue for assessing clinicopathological consequences of DNA hypermethylation in breast cancer.

Breast Neoplasms↗
PubMed2000

Expression of the genetic variants of human alpha-1-acid glycoprotein in cancer.

OBJECTIVES: We have investigated the AAG and its genetic variants concentrations in plasma samples of 61 patients suffering from different types of cancers. DESIGN AND METHODS: The patients were shared out in three groups, breast, lung, and ovary cancers groups. AAG concentration was measured by an immunonephelometric method and the phenotype was determined, after desialylation of plasma by analytical isoelectric focusing. Detection of AAG variants was made by immunoblotting and their proportions were determined by laser densitometry analysis. A population of 74 healthy individuals served as controls. RESULTS: The plasma concentrations of AAG in the breast and lung cancer groups were 2.5 times increased, while in the ovary cancer group, the concentrations were 1.6 times increased. AAG concentrations in the cancer population ranged between 0.45 and 2.85 g/L (mean value 1.12 +/- 0.51 g/L). The proportions of the ORM1 and ORM2 variants were similar to those in the healthy population. In breast and lung cancer groups, the relative concentrations of genetic variants were increased more than 2.5 fold, whereas a 1. 6-fold increase was observed in the ovary cancer group. CONCLUSIONS: These results show that AAG plasma concentrations are increased in these types of cancers and that changes in the expression of the genetic variants of AAG could also occur according to the type of cancer.

Adult↗
PubMed2000

Species associations among larval helminths in an amphipod intermediate host.

Larval helminths that share the same intermediate host may or may not also share the same definitive hosts. If one or more of these helminth species can manipulate the phenotype of the intermediate host, there can be great advantages or severe costs for other helminths resulting from co-occurring with a manipulator, depending on whether they have the same definitive host or not. Among 2372 specimens of the amphipod Echinogammarus stammeri collected from the river Brenta, northern Italy, there was a positive association between two acanthocephalan species with the same fish definitive hosts, the relatively common Pomphorhynchus laevis and the much less prevalent Acanthocephalus clavula. The number of cystacanths of P. laevis per infected amphipod, which ranged from one to five, did not influence the likelihood that the amphipod would also host A. clavula. A third acanthocephalan species, Polymorphus minutus,which matures in birds, showed no association with either of the two other species. These results show that associations among helminth species in intermediate hosts are not random, and are instead the product of selection favouring certain pathways of transmission.

Acanthocephala↗
PubMed2003

A novel functional polymorphism in the PECAM-1 gene (53G>A) is associated with progression of atherosclerosis in the LOCAT and REGRESS studies.

A 53G>A polymorphism identified in the 5' untranslated region (5'UTR) of the platelet endothelial cell adhesion molecule-1 (PECAM-1) gene alters a putative shear stress responsive element (SSRE). PECAM-1 was shown to be responsive to shear stress and transient transfection of human umbilical vein endothelial cell (HUVECs) with two luciferase reporter constructs driven by the PECAM-1 promoter and 5'UTR showed a response of the 53G allele, not the 53A allele, to shear stress. Association between the 53G>A, and the previously published L125V polymorphism, and coronary atherosclerosis was examined in two angiographic studies. The frequencies of the rare alleles of the 53G>A and L125V polymorphisms were 0.01 and 0.49, respectively, in the Lopid Coronary Angiography Trial (LOCAT) study and 0.02 and 0.49, respectively, in the Regression Growth Evaluation Statin Study (REGRESS) study. Compared with 53G homozygotes, carriers of the 53A allele showed less focal progression of disease in the LOCAT study and a similar trend in the diffuse progression of disease in the REGRESS study, whereas no association between L125V and coronary atherosclerosis was observed in either study. These data demonstrate that the PECAM-1 gene is responsive to shear stress in vitro and that decreased PECAM-1 gene expression in 53A carriers may influence reduced progression of vessel stenosis in patients with coronary artery disease.

Aged↗
PubMed2003

A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer.

Here we describe how patterns of gene expression in human tumors have been deconvoluted to reveal a mechanism of action for the cyclin D1 oncogene. Computational analysis of the expression patterns of thousands of genes across hundreds of tumor specimens suggested that a transcription factor, C/EBPbeta/Nf-Il6, participates in the consequences of cyclin D1 overexpression. Functional analyses confirmed the involvement of C/EBPbeta in the regulation of genes affected by cyclin D1 and established this protein as an indispensable effector of a potentially important facet of cyclin D1 biology. This work demonstrates that tumor gene expression databases can be used to study the function of a human oncogene in situ.

CCAAT-Enhancer-Binding Protein-beta↗
PubMed2001

MUC 1: a genetic susceptibility to infertility?

In man and some animals regulation of embryo implantation by endometrial expression of the highly polymorphic MUC 1 mucin has been suggested. We assessed the polymorphism of MUC 1 in women known to be fertile and those with infertility due to suspected failure of embryo implantation. The median of the lower allele size in the infertile group was only 2.5 kb compared with 3.4 kb in the fertile group (p=0.0029, difference 0.9, [95% CI 0.1-1.3]). Women with unexplained infertility might have a genetic susceptibility to failure of embryo implantation due to small MUC 1 allele size.

Adult↗
PubMedDate not supplied

HLA-DRB1 and -DQB1 polymorphism in liver recipients: relationship between HLA-DQB1*0302 allele frequency and acute rejection.

Polymorphism of HLA-DRB1 and HLA-DQB1 loci was performed in fifty-three orthotopic liver graft recipients as well as in 108 unrelated healthy controls. Nonradioactive SSOPs were used to study PCR-amplified DNA from peripheral blood lymphocytes and biopsied material. The comparison frequency for DQB1 alleles did not reveal any significant differences between the total group of liver recipients and controls. However, when the liver recipients were subgrouped according to their rejection episode manifestations, increased and significant frequencies were observed for HLA-DQB1*0302 allele in patients showing acute rejection episodes compared to healthy controls or patients without acute rejection. This relationship did not appear influenced by the amino acid beta alanine residue in the 57th position. On the other hand, the study of the DRB1 allele frequencies did not show significant differences in any study. These results suggest that HLA-DQB1 genes could be important in the liver graft alloresponses, opening a way to a better understanding of the special tolerance state, normally observed in this type of transplant, leading us to consider the possible HLA-DQB1*0302 allele effect on tolerance rupture.

Alleles↗
PubMed2003

Strong association between Saitohin gene polymorphism and tau haplotype in the Polish population.

The saitohin (STH) gene is located in intron 9 of the tau protein gene. It has been postulated that the R allele of Q7R polymorphism at the Saitohin gene is over-represented in the homozygous state in sporadic Alzheimer's disease (AD). Tau protein was implicated in AD pathophysiology and the tau gene haplotype is probably connected with sporadic late-onset Parkinson's disease (PD). We analyzed the STH polymorphism and tau gene haplotype in 100 clinically diagnosed AD cases, 100 PD cases and 100 age-matched healthy controls. We found that the R allele of the STH gene is associated with the H2 haplotype of tau in all cases. Additionally we observed no correlation between R allele frequency and AD or PD.

Aged↗
PubMed1998

Genetic polymorphism of the angiotensin-converting enzyme (ACE) in asthmatic patients.

Angiotensin-converting enzyme (ACE) inactivates bradykinin, substance P and neurokinin A, which are believed to play important roles in the pathogenesis of asthma, especially in neurogenic inflammation. It has recently been shown that an insertion (I)/deletion (D) polymorphism in the ACE gene accounts for variation in serum ACE levels. There are thus three genotypes (insertion homozygote, II; deletion homozygote, DD; heterozygotes, DI). The serum ACE level with the DD type is reported to be about double that of the II type and intermediate in the DI case. In the present study, we examined whether asthma is linked with this ACE gene polymorphism. Seventy-one patients with asthma (27 males and 44 females) and 142 sex- and age-matched healthy controls were determined for their genotype by the polymerase chain reaction (PCR) method. Twenty-five asthmatics demonstrated the II type (35.2%), 37 the DI type (52.1%), and nine the DD type (12.7%). There were no significant differences in the distributions of genotypes and serum ACE levels between healthy controls and patients. No significant differences were evident in serum IgE levels, age at onset, proportion of atopic type patients and severity of asthma among the three genotypes. We did not find any association between asthma and the ACE gene polymorphism in this study.

Asthma↗
PubMed2002

Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster.

BACKGROUND: We characterized RNA transcript levels for the whole Drosophila genome during normal aging. We compared age-dependent profiles from animals aged under full-nutrient conditions with profiles obtained from animals maintained on a low-calorie medium to determine if caloric restriction slows the aging process. Specific biological functions impacted by caloric restriction were identified using the Gene Ontology annotation. We used the global patterns of expression profiles to test if particular genomic regions contribute differentially to changes in transcript profiles with age and if global disregulation of gene expression occurs during aging. RESULTS: Whole-genome transcript profiles contained a statistically powerful genetic signature of normal aging. Nearly 23% of the genome changed in transcript representation with age. Caloric restriction was accompanied by a slowing of the progression of normal, age-related changes in transcript levels. Many genes, including those associated with stress response and oogenesis, showed age-dependent transcript representation. Caloric restriction resulted in the downregulation of genes primarily involved in cell growth, metabolism, and reproduction. We found no evidence that age-dependent changes in transcription level were confined to genes localized to specific regions of the genome and found no support for widespread disregulation of gene expression with age. CONCLUSIONS: Aging is characterized by highly dynamic changes in the expression of many genes, which provides a powerful molecular description of the normal aging process. Caloric restriction extends life span by slowing down the rate of normal aging. Transcription levels of genes from a wide variety of biological functions and processes are impacted by age and dietary conditions.

Aging↗
PubMed2003

The root of the mammalian tree inferred from whole mitochondrial genomes.

Morphological and molecular data are currently contradictory over the position of monotremes with respect to marsupial and placental mammals. As part of a re-evaluation of both forms of data we examine complete mitochondrial genomes in more detail. There is a particularly large discrepancy in the frequencies of thymine and cytosine (T-C) between mitochondrial genomes that appears to affect some deep divergences in the mammalian tree. We report that recoding nucleotides to RY-characters, and partitioning maximum-likelihood analyses among subsets of data reduces such biases, and improves the fit of models to the data, respectively. RY-coding also increases the signal on the internal branches relative to external, and thus increases the phylogenetic signal. In contrast to previous analyses of mitochondrial data, our analyses favor Theria (marsupials plus placentals) over Marsupionta (monotremes plus marsupials). However, a short therian stem lineage is inferred, which is at variance with the traditionally deep placement of monotremes on morphological data.

Animals↗
PubMedDate not supplied

The fallacy of independence testing and the use of the product rule.

Use of the product rule which implies the assumption of within and between locus independence, is still common, particularly in the United States of America. Whilst it may be considered by some to be an acceptable approximation it is not logical to suggest that independence testing somehow "validates" its use. This paper discusses the nature of this fallacy.

DNA Fingerprinting↗
PubMed1987

Spectral analysis of twin time series designs.

The genetic analysis of physiological time series has to accommodate the presence of autocorrelation. This can be accomplished by means of orthogonal transformation of the series, thus enabling the use of standard genetic analysis techniques for the sequence of uncorrelated transforms. In view of the oscillatory character which typifies various physiological time series, it is customary to invoke spectral techniques for the analysis of these series. It can be shown that spectral analysis is an orthogonal transformation that asymptotically resembles principal component analysis. Consequently, standard genetic analysis methods for the uncorrelated spectral transforms may be used. This approach will be illustrated with simulated and real (heart rate) data for univariate twin time series. Furthermore, it will be indicated that the proposed analysis can be readily generalized to multivariate time series.

Electrocardiography↗