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At least 919 records · Page 51Linked to original sources
PubMed1996

Differential effect of H1 variant overexpression on cell cycle progression and gene expression.

To identify functional differences among non-allelic variants of the mammalian H1 linker histones a system for the overexpression of individual H1 variants in vivo was developed. Mouse 3T3 cells were transformed with an expression vector containing the coding regions for the H1c or H10 variant under the control of an inducible promoter. Stable, single colony transformants, in which the normal stoichiometry of H1 variants was perturbed, displayed normal viability, unaltered morphology and no long-term growth arrest. However, upon release from synchronization at different points in the cell cycle transformants significantly overproducing H10 exhibited transient inhibition of both G1 and S phase progression. Overexpression of H1c to comparable levels had no effect on cell cycle progression. Analysis of transcript levels for several cell cycle-regulated and housekeeping genes indicated that overexpression of H10 resulted in significantly reduced expression of all genes tested. Surprisingly, overexpression of H1c to comparable levels resulted in either a negligible effect or, in some cases, a dramatic increase in transcript levels. These results support the suggestion that functional differences exist among H1 variants.

3T3 Cells↗
PubMed1996

Resistance of human immunodeficiency virus type 1 to protease inhibitors: selection of resistance mutations in the presence and absence of the drug.

Inhibitors of the human immunodeficiency virus (HIV) protease are a promising class of antiviral agents that dramatically reduce HIV replication both in culture and in infected patients. However, as for many other antiviral compounds, long-term efficacy of these agents is impeded by the emergence of virus variants with increased resistance to their inhibitory action, following selection of specific mutations in the protease coding sequence. We have studied HIV-1 variants that emerged at different stages of selection in the presence of the C2-symmetrical protease inhibitor ABT-77003. The selection of variants was a gradual process during which mutations accumulated at different sites in the protease, generating virus populations with increasing levels of resistance to the drug. The initially selected viruses had a low level of resistance as well as a markedly reduced replicative capacity. Further accumulation of mutations at secondary sites led to an improvement in both drug resistance and replication. In spite of their reduced infectivity, partially selected virus populations did not readily revert to wild-type when serially passaged in drug-free conditions. Instead, even in the absence of drug, secondary mutations identical to those selected in the presence of the inhibitor continued to emerge. These mutations improved both the intrinsic replicative capacity of the virus and its level of resistance to the inhibitor, suggesting that once committed to drug resistance, readaptation of the enzyme to its natural substrate leads to a reduction of its sensitivity to the inhibitor.

Amino Acid Sequence↗
PubMed1980

Different HLA antigen associations for the functionally active and inactive products of the complement C4F1 allele.

The genetic polymorphism of the fourth component of human complement, C4, was studied in 945 unrelated Caucasian individuals. A third allele of the C4F (Rodgers) locus, termed C4F1 was demonstrated. This allele is characterized using immunofixation electrophoresis, by the presence of an additional fast-moving anodal band of C4 which distinguishes it clearly from the common C4F variant. The allelic frequencies fit the Hardy-Weinberg equilibrium assuming three alleles at the C4F locus: C4F, C4Fo, and C4F1. The functional activity of the C4F variants was investigated using a specific hemolytic overlay technique for C4. It was found that in almost all individuals (75 out of 78), the C4F1 allele codes for a functionally inactive C4 product only when it occurs on an HLA-B17 positive haplotype but that the same allele codes for a functionally active fast variant of C4 when it occurs on an HLS-B37 positive haplotype (18 out of 18). Very strong genetic linkage disequilibrium was observed for the C4F1 allele with HLA-B17 and B37. The active and inactive C4F1 variant also has marked nonrandom gametic association to different alleles of the Bf locus and to HLA-C locus determinants. No further variants of the C4S (Chido) locus have been identified so far. Rodgers (Rg) typing by the plasma inhibition test of anti-Rg antiserum has shown that plasma from individuals homozygous for the C4F1 allele is only able to partially inhibit anti-Rg whereas all C4F positive individuals totally inhibited the reaction.

Alleles↗
PubMed2001

Distribution of the M129V polymorphism of the prion protein gene in a Turkish population suggests a high risk for Creutzfeldt-Jakob disease.

A polymorphism (M129V) at codon 129 of the prion protein gene (PRNP) results in either a methionine residue (Met) or a valine residue (Val) and is known to determine susceptibility for the development of sporadic or acquired Creutzfeldt-Jakob disease (CJD). The distributions of M129V genotypes and alleles in various general populations have been reported and there are clear differences between Western Europeans and East Asians. We analysed the coding sequence of the PRNP gene in 100 healthy Turkish subjects to determine whether the distributions of the M129V genotypes and alleles or other PRNP gene variants in the Turkish population differ from those in other normal populations. Three known polymorphisms but no other gene variants were detected in the PRNP coding sequence of the Turkish individuals. Genotype frequencies at codon 129 were 57% Met/Met, 34% Met/Val and 9% Val/Val, with an allele frequency of 0.740:0.260 Met:Val. These distributions are considerably different from those reported for other normal populations residing in Western Europe and East Asia, except in Crete. The higher frequency of 129 Met-homozygotes in Turkey than in Western Europe suggests that the Turkish are at greater risk of developing CJD.

Adult↗
PubMed2002

Expression of MUCI splice variants correlates with invasive growth of breast cancer cell lines.

On the basis of alternative splicing the human breast cancer associated MUCI gene codes for different protein products. MUCI splice variants A and B have been shown to be determined by a single A/G nucleotide polymorphism (SNP) in exon 2 of the MUCI gene. We now describe two new splice variants C and D and show by that in human breast cancer cell lines there is selective co-expression of these variants, namely co-expression of variants A and D. We have found that the expression of variants C and D is also determined by the same SNP in exon 2. Since the overexpression of MUCI proteins has been associated with increased invasive behavior of cancer cell lines, we quantitatively determined the mRNA expression levels of the splice variants A, B, C, and D in breast cancer cell lines and correlated them with the in vitro invasiveness of these cell lines. We revealed a significant correlation between the lack of MUCI splice variants B and C and the invasiveness of the cell lines tested. Furthermore, we showed that concomitant expression of variants A and D is associated with a GG in the genotype. These findings suggest that the invasive behavior of breast cell lines may depend on different expression patterns of the MUCI gene determined by a genetic polymorphism.

Alternative Splicing↗
PubMedDate not supplied

Genetic variability in the renin-angiotensin system: prevalence of alleles and genotypes.

BACKGROUND: Variants of the human genes coding for renin, angiotensin-converting enzyme (ACE), angiotensinogen (AGT) and the angiotensin II type-I receptor (AT1R) are inconsistently associated with cardiovascular-renal disease, possibly because of genetic differences in the background populations. METHODS: This systematic review of the literature investigated genetic variation in the renin system according to race, sex and age. Across studies with relevant information, multivariate analyses also accounted for the methods of genotyping and the enrollment of subjects as controls, cases or groups studied cross-sectionally. RESULTS: The 185 reviewed reports included 64978 subjects. In five studies (n=989) on the renin gene, the Hind III and Taq I polymorphisms varied with the groups' average age, whereas the Bg I, Bg II and Hind III but not Taq I sites differed according to race. Among 135 studies (n=44697) on the deletion/insertion (D/I) polymorphism of the ACE gene, the frequency of the D allele was 54.0%. Its prevalence was not related to sex and black race, was 49.9% lower in Asians, 10.0% lower in studies relying on I-specific primers, 4.9% higher for each 25-year increment in the average age of the groups studied, and 16.7% higher in cases than controls. Among 12 studies (n=4952) on the T174-->M variant of the AGT gene, the M174 frequency was 11.0%, did not vary according to sex and enrollment group, was 56.7% lower in blacks and 39.5% lower for each 25-year increase in the groups' mean age. Across 44 studies (n=16713) on the M235-->T substitution in the AGT gene, the T235 prevalence was 51.6%. Its frequency was not related to sex and the method of genotyping, tended to be 7.5% lower for each 25-year increase in average age, was from 4.6 to 6.6 times higher in nonwhites than whites and 13.2% higher in cases than controls. Among 13 studies (n=4332) on the A1166-->C variant of the AT1R gene, the C1166 allelic frequency was 25.7%. Its prevalence was independent of the enrollment group, 77.4% lower in Asians, and nearly doubled for each 25-year increment in age. CONCLUSION: With adjustments applied for the subjects' enrollment group and the methods of genotyping, genetic polymorphism in the renin system varies according to race and age, but not sex. One possible application of the present results is to provide allelic and genotypic frequencies, which could be used to assess power, to perform sample size calculations, or to predict selection bias in future studies.

Age Factors↗
PubMed1997

Expression of CD44 splice variants in colorectal cancer.

BACKGROUND: The CD44 gene codes for a family of heavily glycosylated cell surface proteins that have been linked with tumour metastasis. The aim of the study was to analyse the expression of CD44 messenger RNA in colorectal cancer. METHODS: The expression of CD44 variants 2 and 7 in colorectal tumour samples was compared with that in normal colon and lymphocytes from 59 patients using reverse transcription-polymerase chain reaction followed by blot hybridization with exon-specific probes, and a nested polymerase chain reaction. RESULTS: All samples of tumour and metastatic tissue showed complex overexpression of many alternatively spliced products of the CD44 gene. Normal colon, liver and lymphocytes predominantly expressed the standard form of the CD44 molecule (CD44S) with low levels of two or three variants hybridizing to exons v2 and v7. CONCLUSION: Deranged CD44 gene activity in colorectal cancer cells is confirmed. The analysis of CD44 gene expression may provide a promising marker for the early detection of colonic tumours.

Aged↗
PubMedDate not supplied

Expression of a novel RAD23B mRNA splice variant in the human testis.

A gene coding a novel human RAD23B protein named RAD23-like protein B, presumably involved in spermatogenesis, was identified and characterized using a complementary DNA (cDNA) microarray. In the human testis, its expression was 2.33 times higher than it was in the embryo testis, with a particularly high expression in ejaculated human spermatozoa. The full length of this gene is 1548 bp, and the putative protein is 338 amino acids long. This protein is homologous to RAD23B, which is one of two human homologs of Saccharomyces cerevisiae RAD23, and is involved in both nucleotide excision repair (NER) and ubiquitin (Ub)-dependent proteolysis. However, RAD23-like protein B lacks the Ub-like (UbL) domain that functions as a proteasome localization signal. Multiple-tissue expression profile of the messenger RNA (mRNA) that encodes the RAD23-like protein B also showed that it is highly expressed in the human testis and in ejaculated spermatozoa. Our present study indicates that this novel alternative splicing form of RAD23B is correlated with human spermatogenesis.

Amino Acid Sequence↗
PubMed1997

Beta 4 integrin subunit expression is downregulated in low metastatic carcinoma variants.

Organization and expression of the gene coding for beta 4 integrin subunit were investigated in murine carcinoma lines endowed with low and high metastatic potential maintained both in vivo and in vitro. Probes corresponding to either the extracellular or the cytoplasmic domains of the protein were generated and employed for Southern and Northern blot hybridization experiments. Southern blot analysis demonstrates a restriction fragment-length polymorphism between BALB/c and C57BI/6J DNAs. The different genomic organization of the beta 4 gene apparently does not generate variation in mRNA length. Northern blot analysis reveals a 7-kb transcript encoding full-length beta 4 protein and shorter transcripts that apparently correspond to nonfunctional mRNAs. In carcinoma cells endowed with low metastatic capacity, the 7-kb mRNA cannot be revealed in spite of the presence of shorter transcripts. In contrast, the 7-kb transcript is always present in tumor cells endowed with high metastatic capacity. Accordingly, the beta 4 protein is detectable, either by immunofluorescence or by Western blot analyses, only in highly metastatic carcinoma cells. In conclusion, the data presented show that in these murine carcinoma cell lines (i) the 7-kb mRNA is associated with a more invasive phenotype, and (ii) missing expression of the beta 4 integrin subunit in low metastatic carcinoma cells depends, at least in part, on mechanisms acting at a post-transcriptional level. The possibility that beta 4 subunit expression is a consequence of specific differentiation stages of lung carcinoma cells is discussed.

Adenocarcinoma, Bronchiolo-Alveolar↗
PubMed1996

Primary structure of human plasma membrane Ca(2+)-ATPase isoform 3.

The complete coding sequence of the human plasma membrane calcium ATPase (PMCA) isoform 3 was determined from overlapping genomic and cDNA clones. The cDNAs for the two major alternative splice variants 3a (3CII) and 3b (3CI) code for proteins of 1173 and 1220 amino-acid residues, respectively, which show 98% identity with the corresponding rat isoforms. On a multiple human tissue Northern blot, a major PMCA3 transcript of about 7 kb was detected exclusively in the brain, demonstrating the highly restricted pattern of expression of this isoform to human neuronal tissues. With the elucidation of the human PMCA3 primary structure, complete sequence information is now available for the entire family of human PMCA isoforms.

Alternative Splicing↗
PubMed2003

R219K polymorphism of the ABCA1 gene and its modulation of the variations in serum high-density lipoprotein cholesterol and triglycerides related to age and adiposity in white versus black young adults. The Bogalusa heart study.

Mutations in adenosine triphosphate (ATP)-binding cassette transporter 1 (ABCA1) gene have been established as the molecular defect in Tangier disease and familial hypoalphalipoproteinemia, uncommon genetic disorders characterized by deficient or depressed high-density lipoprotein (HDL) cholesterol and increased triglycerides. However, information regarding the frequency of common variants, including Arg219Lys (R219K) within the coding region of the ABCA1 gene and their effect on these phenotypes in the general population is limited. This study examined the frequency and phenotypic effect of R219K variant in a community-based sample of 887 white and 390 black young adults aged 20 to 38 years. The frequency of the variant allele (K219) was higher in blacks than in whites (0.595 v 0.262, P<.001), with carriers (KK+RK) representing 83.8% of blacks versus 44.2% of whites. After adjusting for age, body mass index (BMI), and sex, the genotype effect on HDL cholesterol and natural logarithm of triglycerides was not apparent in whites or blacks. However, significant interaction effects of genotype and age on HDL cholesterol (P<.001) and genotype and BMI on triglycerides (P=.029) were found in whites. Carriers (KK+RK), unlike noncarriers (RR) showed a positive relationship between age and HDL cholesterol (regression coefficient beta=0.28, P=.029 for carriers v beta=-0.18, P=.112 for noncarriers). In addition, the variant allele attenuated the adverse positive relationship between BMI and triglycerides (beta=0.032, P<.001 for carriers v beta=0.046, P<.001 for noncarriers). These results indicate that the K219 allele frequency differs markedly between blacks and whites, and that the variant-allele modulates the association between age and HDL cholesterol, as well as body fatness and triglycerides in a beneficial manner only in whites.

ATP Binding Cassette Transporter 1↗
PubMed2004

Identification and characterization of human glucose transporter-like protein-9 (GLUT9): alternative splicing alters trafficking.

The recently cloned human GLUT9 gene, which maps to chromosome 4p15.3-p16, consists of 12 exons coding for a 540-amino acid protein. Based on a sequence entry (NCBI accession number BC018897) and screening of expressed sequence tags, we have cloned an alternative splice variant of GLUT9 from human kidney cDNA. The RNA of this splice variant consists of 13 exons and codes for a putative protein of 512 amino acids (GLUT9DeltaN). The predicted proteins differ only in their N terminus, suggesting a different subcellular localization and possible physiological role. Screening human tissue RNA by reverse transcription-PCR showed that GLUT9 is expressed mainly in kidney, liver, placenta, and leukocytes, whereas GLUT9DeltaN was detected only in kidney and placenta. The GLUT9 protein localized by immunohistochemistry to human kidney proximal tubules, and subcellular fractionation of human kidney revealed the GLUT9 protein in plasma membranes and high density microsomal membranes. Treatment of kidney membrane proteins with peptide N-glycosidase F showed that GLUT9 and GLUT9DeltaN are expressed in vivo. Localization of GLUT9 and GLUT9DeltaN in three kidney-derived cell lines revealed a plasma membrane distribution for GLUT9 in COS-7 and HEK293 cells, whereas GLUT9DeltaN showed a perinuclear pattern and plasma membrane staining in COS-7 and HEK293 cells, respectively. In polarized Madin-Darby canine kidney cells, GLUT9 trafficked to the basolateral membrane, whereas GLUT9DeltaN localized to the apical membrane. Using heterologous expression of GLUT9 in Xenopus oocytes, GLUT9 appears to be a functional isoform with low affinity for deoxyglucose. Deoxyglucose transport mediated by GLUT9 was not inhibited by cytochalasin B. GLUT9 did not bind cytochalasin B as shown by a cytochalasin B binding assay, indicating a similar behavior of GLUT9 compared with GLUT5.

Alternative Splicing↗
PubMed2005

Comprehensive screening of the thiopurine methyltransferase polymorphisms by denaturing high-performance liquid chromatography.

The drug-metabolizing enzyme thiopurine S-methyltransferase (TPMT) catalyzes the S-methylation of thiopurines such as 6-mercaptopurine, 6-thioguanine, and azathiopurine, which are used as immunosuppressants and in the treatment of acute lymphoblastic leukemia and rheumatoid arthritis. TPMT enzymatic activity is a polymorphic trait, and poor metabolizers may develop life-threatening bone marrow failure. To avoid such adverse effects, the TPMT enzymatic activity in patients' red blood cells (RBCs) is routinely measured prior to thiopurine administration in a limited number of oncology clinics. In the present study, we took advantage of a highly sensitive and specific automated denaturing high-performance liquid chromatography (dHPLC) technique that not only detects known polymorphic alleles, but also identifies previously uncharacterized sequence variants. We developed a dHPLC-based protocol to analyze the entire coding region and validated the protocol to detect all 16 previously described variant alleles. We further analyzed the entire coding region of the TPMT gene in 288 control samples collected worldwide and identified two novel amino acid substitutions Arg163Cys (487C>T) and Arg226Gln (677G>A) within exons 7 and 10, respectively. The clinical application of this comprehensive screening system for examining the entire TPMT gene would help to identify patients at risk for bone marrow failure prior to 6-mercaptopurine therapy.

Chromatography, High Pressure Liquid↗
PubMed1994

Identification of genotypes of hepatitis C virus by sequence comparisons in the core, E1 and NS-5 regions.

Isolates of hepatitis C virus (HCV) show considerable nucleotide sequence variability throughout the genome. Comparisons of complete genome sequences have been used as the basis of classification of HCV into a number of genotypes that show 67 to 77% sequence similarity. In order to investigate whether sequence relationships between genotypes are equivalent in different regions of the genome, we have carried out formal sequence analysis of variants in the 5' non-coding region (5'NCR) and in the genes encoding the core protein, an envelope protein (E1) and a non-structural protein (NS-5). In the E1 region, variants grouped into a series of six major genotypes and a series of subtypes that could be matched to the phylogenetic groupings previously observed for the NS-5 region. Furthermore, core and E1 sequences showed three non-overlapping ranges of sequence similarity corresponding to those between different genotypes, subtypes and isolates previously described in NS-5. Each major genotype could also be reliably identified by sequence comparisons in the well conserved 5'NCR, although many subtypes, such as 1a/1b, 2a/2c and some of those of type 4, could not be reliably distinguished from each other in this region. These data indicate that subgenomic regions such as E1 and NS-5 contain sufficient phylogenetic information for the identification of each of the 11 or 12 known types and subtypes of HCV. No evidence was found for variants of HCV that had sequences of one genotype in the 5'NCR but of a different one in the E1 or NS-5 region. This suggests that recombination between different HCV types is rare or non-existent and does not currently pose a problem in the use of subgenomic regions in classification.

Base Sequence↗
PubMed1994

Detection of hepatocellular carcinoma-specific alpha-fetoprotein by isoelectric focusing.

BACKGROUND: Serum alpha-fetoprotein (AFP) is elevated in up to 80% of patients with hepatocellular carcinoma (HCC). Modestly raised AFP levels (10-400 ng/ml) are also found in patients with nonmalignant liver diseases. In the present study, isoelectric focusing of AFP was used to differentiate the AFP found in patients with HCC. METHODS: To establish the assay conditions, isoelectric focusing was performed on sera from 14 patients with HCC and 13 with nonmalignant liver diseases. Sera was also analyzed under coded conditions from 16 patients with HCC, 14 with chronic active hepatitis (CAH), and 6 with cirrhosis to determine the specificity and sensitivity of the assay in the diagnosis of HCC. RESULTS: Isoelectric focusing of sera from patients with HCC and various non malignant liver diseases identified AFP variants (AFP I-IV). All 14 patients with HCC had AFP variants I and III, and 7 of the 14 also had variant IV. When analyzed in the coded study 13 of the 16 cases of HCC were predicted correctly by the presence of AFP variants III or III and IV. AFP bands III and IV were not discernible in 12 of the 14 patients with CAH and 4 of the 6 with cirrhosis. CONCLUSION: Isoelectric focusing of sera from patients with HCC and nonmalignant liver disease identified two AFP variants apparently specific for HCC. In the setting of borderline elevation of AFP, this technique has a sensitivity of 81% and specificity of 85% for detecting the presence of bands III or IV and may prove suitable for use in a routine laboratory as a screening assay.

Carcinoma, Hepatocellular↗
PubMed2003

Splice variant in TCRzeta links T cell receptor signaling to a G-protein-related signaling pathway.

The T cell receptor zeta chain is required for efficient receptor expression and contributes to T cell receptor-mediated activation of ZAP-70 and PLC-gamma1 as well as other signaling functions. A splice variant of zeta has been described which contains a 3bp insert coding for a glutamine in the cytoplasmic domain. The variant, here designated zeta-Q, is abundant, comprising 20-50% of zeta transcripts in humans, and production of the two isoforms is conserved among distantly related vertebrate species. Analysis of the peptide region in which the insert occurs reveals an unexpected homology with G-protein gamma chains. Transfection studies suggest that disruption in the alignment of three conserved prolines by the insertion of an extra glutamine impairs TCR-mediated PLC activation. Experiments with human lymphocytes suggest that zeta-Q message undergoes upregulation following cellular activation. Our data suggest that regulation of the relative levels of these two transcripts is related to an ancient mechanism which functions to raise the number of receptors required to produce cellular activation during the course of prolonged cellular stimulation, perhaps through a G-protein-related pathway.

Alternative Splicing↗
PubMed1999

Identification of four variants in the tryptophan hydroxylase promoter and association to behavior.

One of the most replicated findings in biological psychiatry is the observation of lower 5-hydroxyindoleacetic acid concentrations, the major metabolite of serotonin, in the brain and cerebrospinal fluid of subjects with impulsive aggression. Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the synthesis of serotonin, however functional variants have not been reported from the coding sequence of this gene. Therefore, we screened the human TPH promoter (TPH-P) for genetic variants which could modulate TPH gene transcription. The TPH-P (2093 nucleotides) was screened for sequence variation by SSCP analysis of 260 individuals from Finnish, Italian, American Caucasian, and American Indian populations. Four common polymorphisms were identified: -7180T>G, -7065C>T, -6526A>G, and -5806G>T (designated as nucleotides upstream of the translation start site). In the Finns, the four polymorphisms had a minor allele frequency of 0.40 and in this population linkage disequilibrium between the four loci was complete. In the other populations the minor allele frequencies ranged from 0.40 to 0.45. TPH -6526A>G genotype was determined in 167 unrelated Finnish offenders and 153 controls previously studied for the TPH IVS7+779C>A polymorphism. A significant association was observed between -6526A>G and suicidality in the offenders. TPH -6526A>G and the previously reported intron seven polymorphism, TPH IVS7+779C>A, exhibited a normalised linkage disequilibrium of 0.89 in Finns. Normalized linkage disequilibrium was reduced in other populations, being 0.49 and 0.21 in Italians and American Indians, respectively. In conclusion, four TPH-P variants were identified which can be used for haplotype-based analysis to localize functional TPH alleles influencing behavior.

Adult↗
PubMed1998

N-terminal splice variants of the NMDAR1 glutamate receptor subunit: differential expression in human and monkey brain.

The distribution of the mRNA coding for the two N-terminal splice variants of the N-methyl-D-aspartate receptor 1 (NMDAR1) subunit of the glutamate NMDA receptor was studied on whole-hemisphere human and macaca fascicularis brain sections by in-situ hybridisation. Synthetic oligonucleotides directed against NMDAR1a and NMDAR1b variants showed a specific distribution that was similar in human and monkey brain, with the NMDAR1a isoform present in the majority of the NMDA receptors, and the NMDAR1b variant present at high levels only in the cortex and dentate gyrus of the hippocampus. The distribution of the mRNAs for the NMDAR1pan and NMDAR1a subunit reported in this study support previous findings in rodent brain, while the restricted distribution of the NMDAR1b variant found in human and monkey suggests some important differences in the composition of the NMDA receptor in rodents and primates.

Aged↗