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Polymorphic variants of NFKB1 and its inhibitory protein NFKBIA, and their involvement in sporadic breast cancer.

Nuclear factor kappa-beta (NF-kappaB) is a transcription factor responsible for modulating the expression of many genes involved in cell proliferation, differentiation, apoptosis and metastasis. NF-kappaB interacts with IkappaB inhibitory proteins to regulate gene expression. This study investigated common variants within the genes coding for NF-kappaB and IkappaB, NFKB1 and NFKBIA, for involvement in sporadic breast cancer. Genotypes were determined in a population of breast cancer affected individuals and age-matched controls. Results do not support an involvement of the tested NFKB1 and NFKBIA polymorphisms in susceptibility to sporadic breast cancer, in the tested Caucasian population.

Breast Neoplasms↗

The genomic structure of the human SPEC1 gene reveals complex splicing and close promoter proximity to the AF1q translocation gene.

SPECs are small Cdc42 signaling molecules. In mammals, two genes, SPEC1 and SPEC2, encode proteins of 79 and 84 amino acid residues, respectively. Here we report the expression and genomic organization of the human SPEC1 gene. Using Northern blot analysis, three major SPEC1 mRNA transcripts of 1.6, 3.3, and 6.3 kb were detected. Identification and sequencing of different sized SPEC1 cDNA clones revealed that the transcript size heterogeneity was due to alternative splicing in the 3'-untranslated region. In addition, a distinct SPEC1 splice variant from within the coding sequence, SPEC1-beta, was identified and detected in a variety of human tissues. Analysis of the genomic organization of SPEC1 revealed that the coding sequence of the SPEC1 isoform was derived from exons 2, 3 and 4, while the SPEC1-beta isoform was derived from exon 2 and a read-through event of intron 2. Examination of the 5'-end of the SPEC1 genomic sequence revealed that AF1q, a previously identified gene involved in translocations with the MLL (mixed-lineage leukemia) gene, was 631 bp away in a head-to-head orientation. This intergenic sequence containing the putative promoter region for both SPEC1 and AF1q genes did not contain a TATA box or CAAT box. Transfection experiments using an AF1q promoter luciferase reporter construct in a variety of cells including Cos1 cells, Jurkat T-cells, MCF-7 breast cancer cells, and NIH-3T3 fibroblasts showed no promoter activity. In contrast, a SPEC1 promoter luciferase reporter construct showed high levels of reporter activity in Cos1 and MCF-7 cells, low activity in NIH-3T3 fibroblasts and no activity in Jurkat T-cells. These promoter analyses suggest that although SPEC1 and AF1q genes share the same promoter region, they are not coordinately regulated.

3T3 Cells↗

The human melanocortin-1 receptor locus: analysis of transcription unit, locus polymorphism and haplotype evolution.

The complete sequence of the MC1R locus has been assembled, the coding region of the gene is intronless and placed within a 12 kb region flanked by the NULP1 and TUBB4 genes. The immediate promoter region has an E-box site with homology to the M-box consensus known to bind the microphthalmia transcription factor (MITF); however, promoter deletion analysis and transactivation studies have failed to show activation through this element by MITF. Polymorphism within the coding region, immediate 5' promoter region and a variable number tandem repeat (VNTR) minisatellite within the locus have been examined in a collection of Caucasian families and African individuals. Haplotype analysis shows linkage disequilibrium between the VNTR and MC1R coding region red hair variant alleles which can be used to estimate the age of these missense changes. Assuming a mean VNTR mutation rate of 1% and a star phylogeny, we estimate the Arg151Cys variant arose 7500 years before the present day, suggesting these variants may have arisen in the Caucasian population more recently than previously thought.

Amino Acid Sequence↗

A novel spliced transcript of human CLAPS2 encoding a protein alternative to clathrin adaptor protein AP17.

Transcripts of genes encoding proteins of clathrin complexes have been reported to undergo tissue-specific alternative splicing. AP17, encoded by human CLAPS2 cDNA, is the small chain of the major clathrin adaptor complex AP-2 associated with mammalian plasma membranes. In this study, two cDNAs were isolated from a cDNA library of human blood cells. Whereas one cDNA encoded AP17, the other cDNA encoded a putative novel protein variant, termed AP17Delta. Both coding regions were completely sequenced. Consisting of 142aa residues, the predicted protein AP17Delta of 12kDa lacks 38aa residues of AP17. Using specific primers for RT-PCR, mRNAs for AP17Delta and AP17 were found in leukocytes and cultured leukemia cells. The finding of a putative intron in a human EST cDNA clone suggests that mRNAs for AP17 and AP17Delta are formed by alternative splicing. In addition, the identity of human and rat AP17 amino acid sequences is demonstrated.

Adaptor Protein Complex 2↗

Influences of matrix metalloproteinase-3 gene variation on extent of coronary atherosclerosis and risk of myocardial infarction.

OBJECTIVES: The aim of this study was to assess matrix metalloproteinase-3 (MMP3) gene variation in relation to the degree of coronary atherosclerosis and risk of myocardial infarction (MI) in patients with coronary artery disease. METHODS: In this study, we systematically screened the promoter and coding regions for sequence variants. All polymorphisms identified were analyzed in 1,240 individuals undergoing coronary angiography. Functional analyses of the polymorphisms were carried out with the use of report assays and electrophoretic mobility shift assays. RESULTS: Six novel polymorphisms were identified. The 6A/6A genotype was associated with greater number of coronary arteries with significant stenosis (odds ratio [OR] 1.52, p = 0.008), whereas the 5A/5A and 5A/6A genotypes were associated with increased risk of MI (OR 2.02 and 1.78, p = 0.016 and 0.032, respectively). A stepwise logistic regression analysis with all polymorphisms taken into account showed that the effect of MI susceptibility was largely attributed to the 5A/6A polymorphism. In a stepwise logistic regression analysis with all haplotypes as independent variables, the most common haplotype (T-5A-A-A-G-A), and two rare haplotypes, all containing the 5A allele, were associated with MI susceptibility. Functional studies showed that the T-5A-A-A-G-A haplotype had a higher promoter activity in macrophages. CONCLUSIONS: These data indicate that the effect of MMP3 gene variation is attributable to the 5A/6A polymorphism and that individuals carrying the 6A/6A genotype may be predisposed to developing atherosclerotic plaques with significant stenosis, whereas those carrying the 5A allele may be predisposed to developing unstable plaques.

Aged↗

Determinants of pathogenicity of echovirus 9 in men: significance of a functional RGD-motif.

In this study, we investigated nine independent echovirus 9 isolates obtained from sick children in 1995. It is discovered that these isolates differ in respect to their pathogenicity for newborn mice indicating that the degree of human pathogenicity of an echovirus 9 variant does not necessarily correlate with mouse pathogenicity. Nevertheless, all virus variants are found to code for an RGD-motif within their VP1 protein. Hence, the RGD-motif and its highly conserved flanking regions are the conditio sine qua non, but, as expected, not sufficient for the mouse-pathogenic character.

Amino Acid Sequence↗

Structure characterization of human RalGDS gene, and the identification of its novel variant.

RalGDS is a guanine nucleotide dissociation stimulator for Ral, which is a member of the Ras GTPase superfamily that regulates cellular proliferation, differentiation and transformation by mediating multiple signal transduction pathways. RalGDS can specifically promote the conversion from an inactive GDP-bound state to an active GTP-bound state for Ral. The cDNA of human RalGDS has been cloned recently. In this paper, by comparison between the gene's genomic and cDNA seqence, we determined the structure of the gene, which showed that the reported human RalGDS transcribed from 18 exons. Furthermore, a novel variant of RalGDS that codes for a protein with a different N-terminus was cloned and identified. Northern hybridization revealed that the novel transcript was of 6.0 kb in length while the transcript previously reported is of 4.0 kb. Both transcripts were ubiquitously expressed in human adult tissues examined, albeit with different amounts. In addition, this novel transcript was proved to be caused by employment of a new exon, designated as exon 1a, instead of the one, designated as exon 1b, in the reported cDNA. Thus, the RalGDS gene consists of at least 19 exons and spanned a 44 kb region. The length between exon 1a and exon 2 was 33 kb, while the length between exon 1b and exon 2 was 8.8 kb.

Amino Acid Sequence↗

Evolution of a trypanosome surface antigen gene repertoire linked to non-duplicative gene activation.

African trypanosomes activate, one at a time, a large set of genes coding for different variant-specific surface antigens (VSAs). These genes have been classed into two groups. In the first group a permanently silent basic gene copy is duplicated and the expression-linked copy (ELC) transposed to an expression site located at a chromosome end. The process is a gene conversion which changes a variable stretch of the preceding ELC. Genes belonging to the second group do not give rise to an additional copy when expressed by a still unknown mechanism. We report here that the gene for antigenic type AnTat 1.6 is located in a telomeric DNA region and is expressed without being duplicated. In clone AnTat 1.6 and the ensuing ones, the ELC of the preceding VSA (AnTat 1.3) is conserved, but in a inactive conformation. Moreover, the AnTat 1.6 gene is lost from the genome of the AnTat 1.6-derived variants, in which the duplication-linked mechanism of gene activation occurs: the gene appears to be replaced by the incoming ELC. These observations show that a trypanosome surface antigen repertoire may evolve by loss and gain of VSA genes, depending on the alternation of the different recombinational mechanism involved in antigenic variation.

Antigens, Surface↗

Analysis of 14q12 microdeletions reveals novel regulatory loci for the neurodevelopmental disorder-related gene FOXG1.

Up to 17% of neurodevelopmental disorders (NDDs) can be explained by pathogenic structural variants (SVs) that disrupt coding regions and elicit gene dosage defects. However, noncoding SVs which can perturb cis-regulatory elements (CREs) and downstream gene expression are understudied. In this study, we describe multiple 14q12 deletions downstream of NDD-related gene FOXG1 in individuals with overlapping phenotypes of FOXG1 haploinsufficiency. We show that deletion of a minimum region of overlap (MRO) reduced FOXG1 expression, disrupted CREs and altered FOXG1's native genomic interactions. Deleting the MRO did not fully eliminate FOXG1 expression, indicating that multiple CREs likely cooperate to regulate FOXG1 and would need to be deleted to completely prevent expression. The transcriptomic profiles of MRO loss overlap in part with FOXG1 loss, including direct FOXG1 targets, indicating converging molecular pathways. These findings expand the scope of FOXG1's complex regulatory region, and more broadly, of regulatory SVs in NDD susceptibility.

Forkhead Transcription Factors↗

Determinants of functional burden pleiotropy and gene dosage responses across human traits.

Pleiotropic and monotonic effects of gene dosage are central to understanding comorbidities in developmental pediatric and psychiatric disorders, yet the underlying biological processes are not well characterized. Here we develop a functional burden analysis to investigate the association of all protein-coding copy-number variants, genome-wide, with 43 complex traits in approximately 500,000 UK Biobank participants. We test variant associations disrupting 172 tissue or cell-type gene sets, finding associations for all traits, which we replicate in the All of Us cohort. Functional burden pleiotropy, defined as the number of traits significantly associated with a gene set, correlates with genetic constraint and is higher for brain than non-brain functions, even after normalizing for genetic constraint. Levels of pleiotropy, measured by burden correlation, are similar in deletions and loss-of-function single-nucleotide variants, and higher than in common variants and duplications. Most gene dosage responses are non-monotonic, with deletions and duplications showing same-direction effects, and monotonic responses decrease with genetic constraint. We observe associations between functional gene sets and traits for either deletions or duplications, but rarely both, with negatively correlated effect sizes. Together, these results link genetic constraint and brain-specific mechanisms to the whole-body multimorbidity of neurodevelopmental and psychiatric conditions.

Humans↗

No evidence for involvement of IL-4R and CD11B from the IBD1 region and STAT6 in the IBD2 region in Crohn's disease.

Linkage studies have identified the inflammatory bowel disease (IBD)1 locus on chromosome 16 and the IBD2 locus on chromosome 12 to be involved in Crohn's disease. NOD2/CARD15 was identified as the gene of interest within the IBD1 region. However, linkage to this region could not be explained by NOD2/CARD15 alone. Here we set out to assess the association of additional candidate genes from the IBD1 and IBD2 loci with Crohn's disease using transmission disequilibrium testing in patient-parent triads. No significant association was observed with genetic variants in the genes coding for interleukin-4 receptor gene (IL-4R), CD11B and signal transducer and activator of transcription type 6 (STAT6). Results for IL-4R were not affected by exclusion of all families carrying one of three risk alleles in NOD2. From this we conclude that IL-4R and CD11B in the IBD1 region and STAT6 in the IBD2 region are not involved in Crohn's disease in this Dutch cohort.

Adult↗

Changes in metabotropic glutamate receptor mRNA levels following global ischemia: increase of a putative presynaptic subtype (mGluR4) in highly vulnerable rat brain areas.

Metabotropic glutamate receptors mediate their intracellular response by coupling to G proteins and may be divided into three subfamilies: mGluR1 and mGluR5, which stimulate phosphatidylinositol hydrolysis; mGluR2 and mGluR3, which are negatively coupled to cyclic AMP formation; and mGluR4 and mGluR6, which also inhibit forskolin-stimulated cyclic AMP formation. The mGluR4 subtypes may represent L-2-amino-4-phosphonobutyrate-sensitive presynaptic autoreceptors, and two alternatively spliced variants of the mGluR4 coding for two receptors with different C termini have been identified. Using in situ hybridization, we measured the levels of mGluR1-mGluR5 mRNA in regions of the rat brain 24 h after transient global ischemia, a time point when no neuronal damage can yet be observed morphologically. In the hippocampus, the mRNA levels for mGluR1, mGluR2, and mGluR5 were decreased, mGluR3 mRNA levels were unchanged, and the mGluR4 mRNA levels were strongly increased. The strongest increase appeared to be in the mRNA encoding mGluR4b. The mGluR4 mRNA was also increased in the parietal cortex, whereas the ventral posteromedial thalamic nucleus showed a small decrease in its mRNA content. These results suggest that vulnerable neurons react to an increased extracellular glutamate concentration by differential regulation of the mRNA for pre- and postsynaptically located metabotropic glutamate receptors.

Animals↗

Polymorphisms of cardiac presynaptic alpha2C adrenergic receptors: Diverse intragenic variability with haplotype-specific functional effects.

The presynaptic alpha2C adrenergic receptors (AR) act to inhibit norepinephrine release in cardiac and other presynaptic nerves. We have recently shown that a genetic variant in the alpha2CAR coding region (Del322-325), which renders the receptor partially uncoupled from Gi, is a risk factor for heart failure. However, variability of heart failure phenotypes and a dominance of Del322-325 in those of African descent led us to hypothesize that other regions of this gene have functional polymorphisms. In a multiethnic population, we found 20 polymorphisms within 4,625 bp of contiguous sequence of this intronless gene encompassing the promoter, 5' UTR, coding, and 3' UTR. These polymorphisms occur in 24 distinct haplotypes with complex organizations, including multiple 5'-upstream polymorphisms in regions known to direct expression, a 3' UTR substitution polymorphism within an insertion/deletion sequence, and the radical coding polymorphism that deletes four amino acids. Relatively low linkage disequilibrium between many polymorphisms, few cosmopolitan haplotypes, prevalent ethnic-specific haplotypes, and substantial genetic divergence among haplotypes was noted. The dysfunctional Del322-325 allele was partitioned into multiple haplotypes, with frequencies of 48% to 2%. The functional implications of the haplotypes were ascertained by whole-gene transfections of human neuronal cells, where haplotype was significantly related (P < 0.001) to expression levels of receptor transcript and protein. Expression varied by as much as approximately 50% by haplotype, and such studies enabled haplotype clustering by phenotypic, rather than genotypic, similarities. Thus, depending on phenotype, expression-specific haplotypes may amplify, attenuate, or dominate the cardiomyopathic effect attributed to the alpha2CDel322-325 marker.

Haplotypes↗

Appetite of an epiphyte: quantitative monitoring of bacterial sugar consumption in the phyllosphere.

We report here the construction, characterization, and application of a bacterial bioreporter for fructose and sucrose that was designed to monitor the availability of these sugars to microbial colonizers of the phyllosphere. Plasmid pP(fruB)-gfp[AAV] carries the Escherichia coli fruB promoter upstream from the gfp[AAV] allele that codes for an unstable variant of green fluorescent protein (GFP). In Erwinia herbicola, this plasmid brings about the accumulation of GFP fluorescence in response to both fructose and sucrose. Cells of E. herbicola (pP(fruB)-gfp[AAV]) were sprayed onto bean plants, recovered from leaves at various time intervals after inoculation, and analyzed individually for GFP content by quantitative analysis of digital microscope images. We observed a positive correlation between single-cell GFP accumulation and ribosomal content as determined by fluorescence in situ hybridization, indicating that foliar growth of E. herbicola occurred at the expense of fructose and/or sucrose. One hour after inoculation, nearly all bioreporter cells appeared to be actively engaged in fructose consumption. This fraction dropped to approximately 11% after 7 h and to approximately 1% a day after inoculation. This pattern suggests a highly heterogeneous availability of fructose to individual E. herbicola cells as they colonize the phyllosphere. We estimated that individual cells were exposed to local initial fructose abundances ranging from less than 0.15 pg fructose to more than 4.6 pg.

Bacterial Proteins↗

Gene duplication and fixed heterozygosity for alcohol dehydrogenase in the diploid plant Clarkia franciscana.

All individuals of the diploid plant Clarkia franciscana, an annual species native to California, have duplicated genes for the dimeric enzyme alcohol dehydrogenase. Since each gene specifies a polypeptide with a distinct charge, the species has a fixed heterozygous phenotype consisting of three isozyme variants. The enzyme is coded by a single gene in closely related species. Clarkia franciscana is highly self-pollinated and monomorphic at all but one of its loci that have been examined. Consequently, the duplication provides enzyme variability in the absence of genetic variability.

Alcohol Oxidoreductases↗

Somatic cell origin of teratocarcinomas.

Malignant teratocarcinomas arise from developmentally totipotent normal stem cells. Whether the targets are embryonal somatic cells or germinal cells has long been a matter of controversy. Past experiments on teratocarcinoma induction by ectopic grafting of early rodent embryos or fetal germinal ridges have remained ambiguous because embryos ordinarily soon form germ cells, and parthenogenetic germ cells form "embryos." In order to interrupt the developmental cycle at its most telling point, day 6 (egg-cylinder stage) mouse embryos of genetically sterile types were grafted; in such grafts, only a terminal residue of totipotent embryonal somatic ("ectoderm") cells is available, and subsequent germ cell development is severely impaired. One graft series, from S1(J)/+ matings, comprised 25% S1(J)/S1(J) presumptive sterile embryos; these grafts formed tumors containing embryonal carcinoma cells as often (47%) as did control +/+ grafts (41%) on the same genetic background. In another series, from W/+ matings, tumors of the sterile W/W genotype were individually identified by means of a closely linked marker, phosphoglucomutase (PGM, EC 2.7.5.1; Pgm-1 locus), coding for electrophoretic enzyme variants and incorporated into the stock. Four tumors were obtained (out of 16) that had the PGM-1D phenotype diagnostic for W/W, and that also contained embryonal carcinoma cells. Therefore, the malignancy arises here in susceptible somatic embryonal stem cells at the terminal stage of their capacity for totipotency. Other teratocarcinomas-whether induced or spontaneous-of ostensible germ-cell origin by parthenogenesis may also depend upon development of the same somatic target cells before neoplastic conversion can occur. A general model based on these experiments is proposed for all malignancies: Malignant transformation of a particular kind of normal stem cell may be possible only when that stem cell has progressed to the threshold of further differentiation.

Animals↗

The human glycine receptor subunit alpha3. Glra3 gene structure, chromosomal localization, and functional characterization of alternative transcripts.

The neuronal glycine receptor is a ligand-gated chloride channel composed of ligand binding alpha and structural beta polypeptides. Homology screening of a human fetal brain cDNA library resulted in the identification of two alternative splice variants of the glycine receptor alpha3 subunit. The amino acid sequence predicted for the alpha3L variant was largely identical to the corresponding rat subunit. In contrast, the novel splice variant alpha3K lacked the coding sequence for 15 amino acids located within the cytoplasmic loop connecting transmembrane spanning region 3 (TM3) and TM4. Using P1 artificial chromosome (PAC) clones, the structure of the GLRA3 gene was elucidated and its locus assigned to human chromosomal bands 4q33-q34 by fluorescence in situ hybridization. Two transcripts of 2.4 and 9 kilobases, corresponding to alpha3L and alpha3K, respectively, were identified and found to be widely distributed throughout the human central nervous system. Structural analysis of the GLRA3 gene revealed that the alpha3K transcript resulted from a complex splice event where excision of the novel exon 8A comprising the alternative sequence of 45 base pairs coincides with the persistence of a large intronic sequence in the 3'-untranslated region. Functional expression in HEK 293 cells of alpha3L and alpha3K subunits resulted in the formation of glycine-gated chloride channels that differed significantly in desensitization behavior, thus defining the cytoplasmic loop as an important determinant of channel inactivation kinetics.

Alternative Splicing↗

1166C mutation of angiotensin II type 1 receptor gene is correlated with umbilical blood flow velocimetry in women with preeclampsia.

OBJECTIVE: To ascertain the frequency of polymorphic variants of the gene coding for angiotensin II type 1 receptor (AT1) and its correlation with umbilical artery (UA) blood flow velocity in a group of women with preeclampsia (PE). STUDY DESIGN: AT1 polymorphism, pulsatility index (PI) in UA, and perinatal outcome in 47 women with PE and in 113 healthy pregnant women were investigated. Investigation of AT1 receptor genotypes was performed by PCR/RFLP assays. PI value has been measured by Doppler velocimetry technique. RESULTS: The overrepresentation of CC homozygotic genotype in PE group (6.4% vs. 2.7%) and the overrepresentation of mutated C allele in the PE group were observed (28.7% vs. 23.0%). Analyzing PI index we observed statistically significant differences between PE and control groups. Comparing PI values in PE group between genotypes: AA vs. AC + CC statistically significant differences (p < 0.05) have been observed. CONCLUSIONS: Observed overrepresentation of mutated C allele of the AT1 gene was correlated with increased blood flow in umbilical artery in women with preeclampsia. Doppler velocimetry might be a useful tool for indication in the high-risk group with overrepresentation of C alleles.

Adult↗