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At least 307 records · Page 17Linked to original sources
PubMed2005

Monoallelic yet combinatorial expression of variable exons of the protocadherin-alpha gene cluster in single neurons.

Diverse protocadherin-alpha genes (Pcdha, also called cadherin-related neuronal receptor or CNR) are expressed in the vertebrate brain. Their genomic organization involves multiple variable exons and a set of constant exons, similar to the immunoglobulin (Ig) and T-cell receptor (TCR) genes. This diversity can be used to distinguish neurons. Using polymorphisms that distinguish the C57BL/6 and MSM mouse strains, we analyzed the allelic expression of the Pcdha gene cluster in individual neurons. Single-cell analysis of Purkinje cells using multiple RT-PCR reactions showed the monoallelic and combinatorial expression of each variable exon in the Pcdha genes. This report is the first description to our knowledge of the allelic expression of a diversified receptor family in the central nervous system. The allelic and combinatorial expression of distinct variable exons of the Pcdha genes is a potential mechanism for specifying neuron identity in the brain.

Animals↗
PubMedDate not supplied

Induction of drug resistance and protein kinase C genes in A2780 ovarian cancer cells after incubation with antineoplastic agents at sublethal concentrations.

We examined the inducibility of drug resistance (MDR1, MRP1, LRP) and protein kinase C (PKC) isozyme (alpha, epsilon, eta, theta, tau, zeta) corresponding genes in A2780 ovarian cancer cells after a 24-hour treatment with adriamycin (ADR), camptothecin (CAM), etoposide (ETO) or vincristine (VCR). Sublethal concentrations of drugs were used to exclude short-term effects caused by selection. Cell cycle analysis was performed to identify possible correlation between resistance factors, PKC isozymes and proliferation. We found a mostly combined induction of MDR1, LRP, PKC tau and PKC zeta by CAM, ETO and VCR. PKC alpha, epsilon, eta and theta gene expression altered variably. Cell cycle analysis showed that A2780 cells responded with a marked G2/M arrest after a 24-hour treatment with CAM, ETO and VCR but an association between the induction of PKC isozymes corresponding genes and proliferation was not seen. Our analysis points to a possible link between atypical PKC tau/PKC zeta and MDR1/LRP in cytostatic stress response of cancer cells.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2006

Impact of transcriptional properties on essentiality and evolutionary rate.

We characterized general transcriptional activity and variability of eukaryotic genes from global expression profiles of human, mouse, rat, fly, plants, and yeast. The variability shows a higher degree of divergence between distant species, implying that it is more closely related to phenotypic evolution, than the activity. More specifically, we show that transcriptional variability should be a true indicator of evolutionary rate. If we rule out the effect of translational selection, which seems to operate only in yeast, the apparent slow evolution of highly expressed genes should be attributed to their low variability. Meanwhile, rapidly evolving genes may acquire a high level of transcriptional variability and contribute to phenotypic variations. Essentiality also seems to be correlated with the variability, not the activity. We show that indispensable or highly interactive proteins tend to be present in high abundance to maintain a low variability. Our results challenge the current theory that highly expressed genes are essential and evolve slowly. Transcriptional variability, rather than transcriptional activity, might be a common indicator of essentiality and evolutionary rate, contributing to the correlation between the two variables.

Animals↗
PubMed1996

Restricted immunoglobulin VH region repertoire in chronic lymphocytic leukemia patients with autoimmune hemolytic anemia.

Between 10% and 25% of chronic lymphocytic leukemia (CLL) patients have episodes of autoimmune hemolytic anemia (AIHA) during the course of their disease. The anti-erythrocyte autoantibodies in most cases are polyclonal and express a different heavy chain isotype than the malignant clone, indicating that they are secreted by normal autoreactive B lymphocytes. To further investigate the pathogenesis of the AIHA in CLL, we analyzed the lg heavy (H) chain variable region genes expressed by leukemic cells from CLL patients with and without AIHA. Two VH genes were preferentially expressed by the leukemic cells in the CLL cases with AIHA and were present in 9 of the 12 investigated cases. The 51p1/DP-10 gene was expressed in 5 of these cases and was absent in the control group of 12 consecutive CLL cases without AIHA, whereas the DP-50 gene was present in 4 CLL-AIHA cases and only once in the control CLL group. A strikingly similar H-chain CDR3 region that contained a single reading frame of the DXP4 DH gene segment, and N-encoded proline at the DH/JH boundary, and a tyrosine-rich region encoded by the JH6 gene segment was observed in four CLL-AIHA cases. The preferential expression of two VH gene segments and a particular CDR3 region by the leukemic cells of patients with AIHA suggests that the antibodies produced by the CLL cells are directly involved in the pathogenesis of the hemolytic anemia.

Amino Acid Sequence↗
PubMed1992

Functional and molecular characterization of single, (4-hydroxy-3-nitrophenyl)acetyl (NP)-specific, IgG1+ B cells from antibody-secreting and memory B cell pathways in the C57BL/6 immune response to NP.

We have used multiparameter flow cytometry to identify a population of IgG1+ IgM- antigen-specific B cells which emerges in spleens of C57BL/6 mice following immunization with the hapten, (4-hydroxy-3-nitrophenyl)acetyl (NP). Characterization of the specificities of IgG1 antibodies produced by single, sorted IgG1+ NP+ cells in both Elispot assays and in microcultures containing lipopolysaccharide, interleukin (IL)-2, IL-4 and IL-5 indicates that the splenic IgG1+ NP+ B cell population includes both IgG1 anti-NP antibody-secreting cells and non-secreting, IgG1+ memory B cells. Each functionally discrete population of IgG1+ B cells expresses a distinctive surface phenotype defined by a wide range of B cell markers. In particular, antibody-secreting, IgG1+ cells were uniquely identified by co-expression of the matrix receptor, syndecan. The NP-specific B cell population emerging in the day 7 primary response was assessed for clonotypic diversity by amplification and direct sequencing of the rearranged V186.2 heavy chain variable region gene expressed by single, ex vivo IgG1+ NP+ lambda+ B cells. Memory B cell clones, distinguished by junctional diversity, carried either no mutation or a single mutation within rearranged V186.2, suggesting isolation of these cells at the onset of the hypermutation mechanism. This novel approach, therefore, allows the direct and unambiguous identification and characterization of individual B cell clonotypes during their initial selection and activation in antibody responses in vivo.

Animals↗
PubMed1990

Abnormalities of lymphokine gene expression in patients with common variable immunodeficiency.

Common variable immunodeficiency (CVI) is a syndrome characterized by hypogammaglobulinemia, recurrent bacterial infections, and increased occurrence of both autoimmune disease and malignancy. In our study we examine the expression of lymphokine genes in mitogen-activated T cells from four patients with CVI. T cells from patients with CVI did not differ significantly from normals in total T cell number, CD4/CD8 ratio, CD45R expression, or proliferation in response to PHA. However, T cells from this group of patients did exhibit significant abnormalities of mitogen-induced lymphokine gene expression. T cells from patients exhibited significantly decreased expression of IL-2, IL-4, IL-5, and IFN-gamma when compared to normal controls. In contrast to these abnormal findings, mitogen-activated T cells from patients with CVI expressed normal amounts of IL-2R alpha and c-myc suggesting that these patients have a selective abnormality of T cell activation. Furthermore, it is likely that the deficient production of IFN-gamma by patient T cells is partially due to the abnormality of IL-2 production as the levels of IFN-gamma mRNA detected during the initial IL-2-independent phase of T cell activation were normal and the addition of exogenous rIL-2 was able to normalize IFN-gamma production by PHA-stimulated patient cells. Finally, supernatants from PHA-activated cultures of patients PBMC were deficient in their ability to support Ig secretion by Staphylococcus A Cowan's-activated normal B cells suggesting that these T cell abnormalities may contribute to the pathogenesis of this syndrome.

Antigens, Differentiation, T-Lymphocyte↗
PubMed1994

Clonotypic dominance and variable gene elements of pathogenic anti-DNA autoantibodies from a single patient with lupus.

This study explores the usage and diversity of the variable gene elements expressed by human lupus antibodies to DNA bearing the 0-81 idiotype, a marker of pathogenic anti-DNA autoantibodies. Rather than studying DNA-specific clonotypes from different patients, a panel of idiotype positive anti-DNA autoantibody-secreting clones from a single individual were analysed. By cloning and nucleotide-sequencing the heavy-chain variable gene segments, evidence was found for dominance of clonotypic patterns. Also noted was a high rate of diversification among the variable (VH), diversity (DH) and junctional (JH) gene segments utilized, with a pattern of mutations indicative of antigenic selection. These features suggest that the clones secreting the lupus pathogenic autoantibodies have been selected over multiple generations through an affinity-maturation process that is reminiscent of antigen-driven immune responses.

Adult↗
PubMed1986

The velo-cardio-facial (Shprintzen) syndrome. Clinical variability in eight patients.

Eight patients (three sporadic, five from two families) with the velo-cardio-facial syndrome (VCFS) or Shprintzen syndrome are reported. Major clinical findings of this syndrome include a characteristic pattern of facial dysmorphisms, cleft palate, cardio-vascular malformations, and (mostly mild-to-moderate) mental retardation or learning difficulties. The syndrome probably is caused by a dominant gene with very variable expression. From previous reports mostly ascertained from cardio-vascular or cleft palate clinics, the incidence of cleft palate and heart defects was calculated to be 98% and 82%, respectively. Out of eight patients of this study who were diagnosed mainly through their pattern of facial dysmorphisms, only two and four had clefts and heart defects, respectively, further demonstrating the variability in the expression of this gene. Similarly, mental retardation, noted in 100% of previous publications, was not present in all of our patients. In two instances, examination of the mother revealed that she probably carried the mutant gene, but that she showed a milder clinical expression than the index patient. It is suggested that careful family investigations should be performed following detection of an index patient, and that the rate of fresh mutations might be not as high as previously assumed.

Abnormalities, Multiple↗
PubMed2003

Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids.

We have explored compositional variation at synonymous (codon usage) and nonsynonymous (amino acid usage) positions in three complete genomes of Buchnera, endosymbiotic bacteria of aphids, and also in their orthologs in Escherichia coli, a close free-living relative. We sought to discriminate genes of variable expression levels in order to weigh the relative contributions of mutational bias and selection in the genomic changes following symbiosis. We identified clear strand asymmetries, distribution biases (putative high-expression genes were found more often on the leading strand), and a residual slight codon bias within each strand. Amino acid usage was strongly biased in putative high-expression genes, characterized by avoidance of aromatic amino acids, but above all by greater conservation and resistance to AT enrichment. Despite the almost complete loss of codon bias and heavy mutational pressure, selective forces are still strong at nonsynonymous sites of a fraction of the genome. However, Buchnera from Baizongia pistaciae appears to have suffered a stronger symbiotic syndrome than the two other species.

Amino Acids↗
PubMed2005

Mobile classification in microarray experiments.

In a homogeneous group of samples, there are genes whose expression variations can be attributed to factors other than experimental errors. These factors can include natural biological oscillations or metabolic processes. These genes are rarely classified as 'interesting' based on their variability profile. However, their dynamic behaviour can tease out important clues about naturally occurring biological processes in the organism under study and can be used for group classification. Dynamical discriminate function analysis was developed on the concept that stable classification parameters (roots) can be derived from highly variable gene-expression data. Stability of these combinations implies a strongly compensatory relationship that may divulge functional interconnections.

Colitis, Ulcerative↗
PubMed1997

Para Bombay phenotype--a case report.

Bombay phenotype is peculiar in that red cells are not agglutinated by antisera A, B or H; while serum contains anti A, B and H. Existence of modifying genes at independent loci with variable expression of ABO genes is postulated. We report here a case of partial suppression where antigens could be detected by elution tests and unlike classical Bombay type, normal amount of appropriate blood group substances were present in saliva. This case of para Bombay phenotype was detected as a result of discrepancy in cell and serum group ng. This highlights the importance of both forward and reverse grouping in ABO testing.

ABO Blood-Group System↗
PubMedDate not supplied

Real-time RT-PCR and cDNA macroarray to study the impact of the genetic polymorphism at the alphas1-casein locus on the expression of genes in the goat mammary gland during lactation.

Milk fat has a large effect on nutritional, technological and sensorial properties of milk products. The milk fat content and composition are modulated by genetics and nutritional factors and imply a large number of enzymes. The regulation of their gene expression in the mammary gland still needs to be clarified. An association between the extensive polymorphism at the alphas1-casein (alphas1-Cas) locus and both the lipid content and the characteristics of this fraction in caprine milk has been demonstrated. In order to decipher the mechanism responsible for this impact, a quantification of the transcripts of four lipogenic key enzymes (acetyl-CoA carboxylase, fatty acid synthase, lipoprotein lipase and stearoyl-CoA desaturase) was performed using real-time RT-PCR, suggesting an absence of association between the alphas1-Cas genotype and expression variability of the studied genes. This approach has been completed by a more global analysis using a first generation of ruminant macroarray gathering 400 gene probes. The comparison of the expression profiles of lactating goat alphas1-Cas A/A (strong allele) and F/F (defective allele) mammary gland allowed to confirm the expected variability in the expression of known genes (such as those encoding the alphas1-casein) in ruminant mammary tissues as well as to identify up- and down-regulated genes. A second generation of ruminant cDNA macroarray extended to a few thousands of genes is currently in progress and will be applied to study different factors such as the nutritional regulation of gene expression in the mammary gland.

Alleles↗
PubMed2000

A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.

Approximately 12 X-Y homologous gene pairs have been identified in the non-recombining portions of human sex chromosomes. These X-Y gene pairs fall into two categories. In the first category, both X and Y homologs are ubiquitously expressed. In the second category, the X homolog is ubiquitously expressed, whereas the Y homolog is expressed exclusively in the testis. Here we describe a family of human X-Y genes that cannot be assigned to either category. Designated VCX / Y ( Variable Charge X / Y; VCY previously known as BPY1 ), this gene family has multiple members on both X and Y, and all appear to be expressed exclusively in male germ cells. Members of the VCX / Y family share a high degree of sequence identity, with the exception that a 30 nucleotide unit is tandemly repeated in X-linked members but is present only once in Y-linked members. These atypical features suggest that the VCX / Y family has evolved in a manner previously unrecognized for mammalian X-Y genes. We also found that a copy of VCX is present in CRI-S232, a previously described genomic fragment derived from the X chromosome. Studies have shown that aberrant recombination between arrays of CRI-S232-homologous repeats flanking the steroid sulfatase ( STS ) gene results in STS deletion, which is manifested clinically as X-linked ichthyosis. The revelation that CRI-S232 contains VCX offers a more precise description of the genetic etiology of X-linked ichthyosis: it results from aberrant recombination between VCX gene arrays that flank the STS locus.

Adult↗
PubMed2005

Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data.

DNA microarray technology provides a promising approach to the diagnosis and prognosis of tumors on a genome-wide scale by monitoring the expression levels of thousands of genes simultaneously. One problem arising from the use of microarray data is the difficulty to analyze the high-dimensional gene expression data, typically with thousands of variables (genes) and much fewer observations (samples), in which severe collinearity is often observed. This makes it difficult to apply directly the classical statistical methods to investigate microarray data. In this paper, total principal component regression (TPCR) was proposed to classify human tumors by extracting the latent variable structure underlying microarray data from the augmented subspace of both independent variables and dependent variables. One of the salient features of our method is that it takes into account not only the latent variable structure but also the errors in the microarray gene expression profiles (independent variables). The prediction performance of TPCR was evaluated by both leave-one-out and leave-half-out cross-validation using four well-known microarray datasets. The stabilities and reliabilities of the classification models were further assessed by re-randomization and permutation studies. A fast kernel algorithm was applied to decrease the computation time dramatically. (MATLAB source code is available upon request.).

Acute Disease↗
PubMedDate not supplied

[Gene expression profile of medullary thyroid carcinoma--preliminary results].

INTRODUCTION: Medullary thyroid carcinoma occurs both as a sporadic and a familial disease. Inherited MTC (iMTC) patients usually exhibit better prognosis than patients with sporadic form of MTC (sMTC), however, in both subtypes the outcome is unpredictable. No molecular markers contributing to the prognosis or predicting the type of therapy have been introduced to clinical practice until now. The aim of this study was to analyze gene expression pattern of MTC by high density oligonucleotide microarray. MATERIAL AND METHODS: 24 samples were studied: 12 MTC and 12 corresponding normal tissues, (Affymetrix HG-U 133A). Among MTC patients there were half inherited cases and half sporadic ones. RESULTS: First, the differences between MTC and thyroid tissue were analyzed by Singular Value Decomposition (SVD) which indicated three main modes determining the variability of gene expression profile: the first two were related to the tumor/normal tissue difference and the third one was related to the immune response. The characteristic expression pattern, beside of numerous changes within cancer- related genes, included many up-regulated genes specific for thyroid C cells. Further analysis of the second component revealed two subgroups of MTC, but the subdivision was not related to the iMTC/sMTC difference. Recursive Feature Replacement (RFR) confirmed the very similar expression profile in both forms of MTC. With subsequent ANOVA analysis some genes with differential expression could be specified, among them monoamine oxidase B (MAOB) and gamma-aminobutyric acid receptor (GABRR1) which were consistently up-regulated in sMTC. In contrary, some genes involved in regulation of cell proliferation: opioid growth factor receptor(OGFR) and synaptotagmin V (SYT 5) were up-regulated in iMTC. CONCLUSIONS: The obtained data indicate a very similar gene expression pattern in inherited and sporadic MTC. Minor differences in their molecular profile require further analysis.

Biomarkers, Tumor↗
PubMed1986

Characteristic craniofacial appearance and brachytelephalangy in a mother and son with Kallman syndrome in the son.

We report on a mother and son with a similar facies characterized by a square forehead, small nose, telecanthus, and thin upper lip. They both had a similar metacarpal-phalangeal profile characterized by marked brachytelephalangy. They were both short in comparison to other family members, and the son had hypogonadotropic-hypogonadism and anosmia. We favor the hypothesis of a single autosomal dominant gene with variable expression of the hypogonadism and anosmia, although there are alternative explanations for the combination.

Adolescent↗
PubMed2005

Polymorphisms in DNA repair genes as risk factors for spina bifida and orofacial clefts.

Repairing DNA damage is critical during embryogenesis because development involves sensitive periods of cell proliferation, and abnormal cell growth or death can result in malformations. Knockout mouse experiments have demonstrated that disruption of DNA repair genes results in embryolethality and structural defects. Studies using mid-organogenesis rat embryos showed that DNA repair genes were variably expressed. It is hypothesized that polymorphisms that alter the functionality of DNA repair enzymes may modify the risk of malformations. We conducted a case-control analysis to investigate the relationship between DNA repair gene polymorphisms and the risk of spina bifida and oral clefts. Newborn screening blood spot DNA was obtained for 250 cases (125 spina bifida, 125 oral clefts) identified by the California Birth Defects Monitoring Program, and 350 non-malformation controls identified from birth records. Six single nucleotide polymorphisms of five DNA repair genes representing three distinct repair pathways were interrogated including: XRCC1 (Arg399Gln), APE1 (Asp148Glu), XRCC3 (Thr241Met), hOGG1(Ser326Cys), XPD (Asp312Asn, Lys751Gln). Elevated or decreased odds ratios (OR, adjusted for race/ethnicity) for spina bifida were found for genotypes containing at least one copy of the variant allele for XPD [751Gln, OR = 1.62; 95% confidence interval (CI) = 1.05-2.50] and APE 148 (OR = 0.58; CI = 0.37-0.90). A decreased risk of oral clefts was found for XRCC3 (OR = 0.62; CI = 0.39-0.99) and hOGG1 (326 Cys/Cys, OR = 0.22; CI = 0.06-0.78). This study suggested that polymorphisms of DNA repair genes, representing different major repair pathways, may affect risk of two major birth defects. Future, larger studies, examining additional repair genes, birth defects, and interaction with exposures are recommended.

Alleles↗
PubMed2005

Vasopeptidase inhibition peri- and post-MI in Zucker insulin resistant rats: effect on MI size, arrhythmias, remodeling, function and fetal gene expression.

Mortality peri-myocardial infarction (MI) is increased with insulin resistance. As the vasopeptidase inhibitor (VPI) omapatrilat improves insulin sensitivity, it may be beneficial peri-MI in Zucker Insulin Resistant rats (ZIR). ZIR rats (n = 228) received omapatrilat 10 mg/kg/day, 7 days pre-MI, to 38 days post-MI, or control. Twenty-four protocol (n = 72): a subgroup of rats received the kinin receptor antagonist icatibant. Ambulatory ECG recordings, and MI size were evaluated. Thirty-eight-day protocol (n = 156): left ventricular (LV) remodeling, cardiac hemodynamics, morphology, infarct size, and RT-PCR for GLUT-4 and fetal genes were measured. Omapatrilat improved post-MI survival 24 h (62% vs 38%, P = 0.0007) which was maintained 38 days. There was a kinin-induced reduction of ventricular arrhythmias and there appeared to be a kinin-independent reduction in MI size (23.5 +/- 2.4% vs 17.0 +/- 2.2%, P = 0.053) for 24-h post-MI. Omapatrilat reduced but did not prevent LV dilatation, dysfunction, and fetal gene expression 38 days post-MI. Omapatrilat did not prevent reduced cardiac GLUT-4 expression. In ZIR rats, mortality post-MI is reduced by omapatrilat, due and a kinin-dependent reduction in ventricular arrhythmias and possibly a kinin-independent reduction in MI size. Ventricular dilatation, dysfunction, and fetal gene expression are variably attenuated but not prevented.

Actins↗