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At least 1,135 records · Page 63Linked to original sources
PubMed2006

Microarray-based survey of CpG islands identifies concurrent hyper- and hypomethylation patterns in tissues derived from patients with breast cancer.

Maintenance of CpG island methylation in the genome is crucial for cellular homeostasis and this balance is disrupted in cancer. Our rationale was to compare the methylation of CpG islands in tissues (tumor, healthy breast and blood) from patients with breast cancer. We studied 72 genes in 103 samples using microarray hybridization and bisulfite sequencing. We observed tumor specific hyper- or hypomethylation of five genes; COL9A1, MT1A, MT1J, HOXA5 and FLJ45983. A general drop of methylation in COL9A1 was apparent in tumors, when compared with blood and healthy breast tissue. Furthermore, one tumor displayed a complete loss of methylation of all five genes, suggesting overall impairment of methylation. The downstream, evolutionary conserved island of HOXA5 showed hypomethylation in 18 tumors and complete methylation in others. This CpG island also displayed a semimethylated state in the majority of normal breast samples, when compared to complete methylation in blood. Distinct methylation patterns were further seen in MT1J and MT1A, belonging to the metallothionein gene family. The CpG islands of these genes are spaced by 2 kb, which shows selective methylation of two structurally and functionally related genes. The promoters of FLJ45983 and MT1A were methylated above 25% in 18 primary and metastatic tumors. Concurrently, there was also >10% methylation of healthy breast tissue in 11 and 5 samples, respectively. This suggests that the methylation process for the latter two genes takes place already in normal breast cells. Our results also point to a considerable heterogeneity of epigenetic disturbance in breast cancer. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

Breast Neoplasms↗
PubMed2007

Identification and characterization of GFAPkappa, a novel glial fibrillary acidic protein isoform.

Glial fibrillary acidic protein (GFAP) is the principal component of the intermediary filaments in mature astrocytes of the central nervous system (CNS). The protein consists of three domains: the head, the coiled-coil, and the tail. Here, we describe the isolation of an evolutionary conserved novel GFAP isoform, GFAPkappa, produced by alternative splicing and polyadenylation of the 3'-region of the human GFAP pre-mRNA. As a consequence, the resulting human GFAPkappa protein harbors a nonconserved C-terminal tail sequence distinct from the tails of GFAPalpha, the predominant GFAP isoform, and GFAPepsilon, an isoform which also results from alternative splicing. The head and coiled-coil rod domains are identical between the three GFAP isoforms. Interestingly, GFAPkappa is incapable of forming homomeric filaments, and increasing GFAPkappa expression levels causes a collapse of intermediate filaments formed by GFAPalpha. In searching for a biological relevance of GFAPkappa, we noticed that mRNA expression levels of GFAPalpha, GFAPepsilon, and GFAPkappa are gradually increased during development of the embryonic pig brain. However, whereas the GFAPalpha/GFAPepsilon ratio is constant, the GFAPkappa/GFAPepsilon ratio decreases during brain development. Furthermore, in glioblastoma tumors, an increased GFAPkappa/GFAPepsilon ratio is detected. Our results suggest that the relative expression level of the GFAPkappa isoform could modulate the properties of GFAP intermediate filaments and perhaps thereby influencing the motility of GFAP positive astrocytes and progenitor cells within the CNS.

Alternative Splicing↗
PubMed2005

Analysis of ISG expression in chronic hepatitis C identifies viperin as a potential antiviral effector.

Interferon (IFN) alpha inhibits hepatitis C virus (HCV) replication both clinically and in vitro; however, the complete spectrum of interferon-stimulated genes (ISGs) expressed in the HCV-infected liver or the genes responsible for control of HCV replication have not been defined. To better define ISG expression in the chronically infected HCV liver, DNA microarray analysis was performed on 9 individuals with chronic hepatitis C (CHC). A total of 232 messenger RNAs were differentially regulated in CHC compared with nondiseased liver controls. A significant proportion of these were potential ISGs that were transcriptionally elevated, suggesting an ongoing response to endogenous IFN and/or double-stranded RNA. One ISG significantly elevated in all patients was viperin, an evolutionary conserved ISG that has antiviral activity against human cytomegalovirus. Stimulation of Huh-7 and HepG2 cells with IFN-alpha or -gamma revealed viperin is predominantly a type I ISG. Furthermore, viperin expression could also be induced following transfection of Huh-7 cells with either poly(I:C) or HCV RNA. Transient expression of viperin in cells harboring the HCV genomic replicon resulted in a significant decrease in HCV replication, suggesting that viperin has anti-HCV activity. In conclusion, even in the face of a persistent HCV infection, there is an active ISG antiviral cellular response, highlighting the complexity of the host viral relationship. Furthermore, ISG viperin has anti-HCV activity in vitro; we postulate that viperin, along with other ISGs, acts to limit HCV replication.

Antiviral Agents↗
PubMed2002

Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein.

TP53 encodes p53, which is a nuclear phosphoprotein with cancer-inhibiting properties. In response to DNA damage, p53 is activated and mediates a set of antiproliferative responses including cell-cycle arrest and apoptosis. Mutations in the TP53 gene are associated with more than 50% of human cancers, and 90% of these affect p53-DNA interactions, resulting in a partial or complete loss of transactivation functions. These mutations affect the structural integrity and/or p53-DNA interactions, leading to the partial or complete loss of the protein's function. We report here the results of a systematic automated analysis of the effects of p53 mutations on the structure of the core domain of the protein. We found that 304 of the 882 (34.4%) distinct mutations reported in the core domain can be explained in structural terms by their predicted effects on protein folding or on protein-DNA contacts. The proportion of "explained" mutations increased to 55.6% when substitutions of evolutionary conserved amino acids were included. The automated method of structural analysis developed here may be applied to other frequently mutated gene mutations such as dystrophin, BRCA1, and G6PD.

Amino Acid Substitution↗
PubMed2001

Identification of novel RP2 mutations in a subset of X-linked retinitis pigmentosa families and prediction of new domains.

X-linked Retinitis Pigmentosa (XLRP) shows a huge genetic heterogeneity with almost five distinct loci on the X chromosome. So far, only two XLRP genes have been identified, RPGR (or RP3) and RP2, being mutated in approximately 70% and 10% of the XLRP patients. Clinically there is no clearly significative difference between RP3 and RP2 phenotypes. In the attempt to assess the degree of involvement of the RP2 gene, we performed a complete mutation analysis in a cohort of patients and we identified five novel mutations in five different XLRP families. These mutations include three missense mutations, a splice site mutation, and a single base insertion, which, because of frameshift, anticipates a stop codon. Four mutations fall in RP2 exon 2 and one in exon 3. Evidence that such mutations are different from the 21 RP2 mutations described thus far suggests that a high mutation rate occurs at the RP2 locus, and that most mutations arise independently, without a founder effect. Our mutation analysis confirms the percentage of RP2 mutations detected so far in populations of different ethnic origin. In addition to novel mutations, we report here that a deeper sequence analysis of the RP2 product predicts, in addition to cofactor C homology domain, further putative functional domains, and that some novel mutations identify RP2 amino acid residues which are evolutionary conserved, hence possibly crucial to the RP2 function.

Amino Acid Sequence↗
PubMed2006

Sub-Saharan African coding sequence variation and haplotype diversity at the NAT2 gene.

A total of 530 chromosomes from 12 sub-Saharan African populations were sequenced at the human arylamine N-acetyltransferase NAT2 gene. We identified seven novel non-synonymous mutations observed at low frequencies (<11%) in our African multi-ethnic panel. By using algorithms based on evolutionary conservation, two mutations (c.70T>A [p.L24I] and c.578C>T [p.T193M]) for which the activity of their encoded protein has never been determined, were predicted to entail a potentially damaging effect on protein activity. In addition, approximately 5% of the overall NAT2 African haplotypes presented an unknown functional effect. More interestingly, NAT2 haplotype frequencies and acetylation status inference revealed that the hunter-gatherer Western Pygmies and !Kung San were mainly composed of fast and intermediate acetylators, in clear contrast with most agriculturalist populations. These observations highlight the need of a detailed genetic characterization of African populations at this locus to adapt medical treatment, such as the antitubercular isoniazid, to individual/population make-up in the most effective manner.

Africa South of the Sahara↗
PubMed2003

Frequent downregulation of DMBT1 and galectin-3 in epithelial skin cancer.

DMBT1 and galectin-3 are potential interacting proteins with presumably complex roles in tumorigenesis. While at present a variety of mechanisms are discussed for DMBT1 and its participation in cancer, galectin-3 is commonly known to exert tumor-promoting effects. However, in vitro studies in a rodent system have suggested that DMBT1/galectin-3 interaction in the ECM triggers epithelial differentiation, which would point to tumor-suppressive properties. To improve the understanding of DMBT1/galectin-3 action in cancer, we carried out studies in skin cancer of different origins. Mutational analyses of DMBT1 identified a missense mutation in 1 of 13 melanoma cell lines. It led to an exchange of an evolutionary conserved proline residue for serine and located within the second CUB domain of DMBT1. Immunohistochemical analyses demonstrated absence of DMBT1/galectin-3 expression from melanocytes but induction of DMBT1 expression in 1 of 8 nevi and 1 of 11 melanomas and of galectin-3 expression in 3 of 8 nevi and 4 of 8 melanomas. These data suggest that DMBT1 and galectin-3 are unlikely to act as classical tumor suppressors in melanomas. DMBT1 and galectin-3 appear to be secreted to the ECM by epithelial cells within the epidermis and the hair follicle. Compared to the flanking normal epidermis, skin tumors of epithelial origin frequently displayed downregulation of DMBT1 (18 of 19 cases) and galectin-3 (12 of 12 cases). Thus, loss of DMBT1/galectin-3 expression may play a role in the genesis of epithelial skin cancer. This would support the view that galectin-3 can exert tumor-suppressive effects in certain scenarios, and DMBT1/galectin-3-mediated differentiation represents a candidate mechanism for this effect.

Agglutinins↗
PubMed2005

Overexpression of the small transmembrane and glycosylated protein SMAGP supports metastasis formation of a rat pancreatic adenocarcinoma line.

Small cell transmembrane and glycosylated protein (SMAGP) was recently identified in the metastasizing rat pancreatic adenocarcinoma line BSp73ASML. SMAGP, an evolutionary conserved transmembrane protein, is expressed on lateral epithelial cell membranes. SMAGP expression was restricted to or was upregulated in several metastasizing as compared to nonmetastasizing human and rat tumor lines. In contrast to nontransformed tissue, SMAGP was mainly expressed in the cytoplasm, as has already been described for high-grade human colorectal cancer. This raised the question on the impact of SMAGP on tumor progression. To answer the question, metastasis formation was evaluated in the nonmetastasizing rat pancreatic adenocarcinoma subline BSp73AS (AS), which was stably transfected with SMAGP cDNA (AS-SMAGP). Cytoplasmic SMAGP expression promoted cell agglomeration, but inhibited tumor cell proliferation, adhesion to and migration toward vitronectin and matrigel invasion, which was accompanied by a failure of actin reorganization. AS-SMAGP clones strongly promoted metastasis formation by dislodgment of normal tissue; 82% of rats developed lymph node metastasis as compared to 22% of rats receiving AS or mock-cDNA-transfected AS cells. The incidence of lung metastasis was increased from 6% in AS to 98% in AS-SMAGP tumor-bearing rats. Thus, SMAGP strongly promotes tumor progression. This likely is due to redistribution from the plasma membrane into the cytoplasm. SMAGP redistribution does not only facilitate tumor cell detachment from neighboring cells and the extracellular matrix, but obviously contributes actively by a not yet defined mechanism to tumor cell agglomeration and capillary plugging.

Adenocarcinoma↗
PubMed1992

Over-expression of p53 nuclear oncoprotein in colorectal adenomas.

p53 is a nuclear phosphoprotein which controls normal cell growth. Normal p53 protein is undetectable by standard immunohistochemical staining and the over-expression found in neoplastic cells correlates with the presence of point mutations of evolutionary conserved regions of the p53 gene. We examined the expression of p53 protein in a series of 36 colorectal adenomas (13 tubular, 17 tubulovillous, 6 villous) showing different degrees of dysplasia (11 mild, 19 moderate, 6 severe), 11 moderately differentiated adenocarcinomas (6 Duke's A, 4 Duke's B, 1 Duke's C) and 5 metaplastic polyps using the polyclonal antibody CM1 which recognises p53 protein in conventionally fixed and processed histological material. We found that 15 out of 36 colorectal adenomas showed p53 immunoreactivity, although in 4 positive cases (26%) the staining was very focal (less than 0.1% positive cells). More than 80% of severely dysplastic adenomas showed strong p53 immunoreactivity and this over-expression was correlated with increased cell proliferative rate as detected by the proliferating-cell-nuclear-antigen (PCNA) staining. p53 nuclear staining was also seen in 8 out of 11 (65%) colorectal adenocarcinomas as previously shown. Our data suggest that the p53 gene mutation, with the subsequent over-expression of the protein, occurs in colorectal adenomas and may therefore be a fundamental genetic event underlying the dysplasia and loss of proliferative control that are characteristic of adenomas with malignant potential.

Adenoma↗
PubMed1984

Amino acid sequence of the carboxy-terminal part of an acidic type I cytokeratin of molecular weight 51 000 from Xenopus laevis epidermis as predicted from the cDNA sequence.

The DNA sequence of a clone from a cDNA library made from Xenopus laevis skin is described. This sequence represents the 3'-terminal end of an mRNA which codes for an epidermal cytokeratin polypeptide of mol. wt. 51 000 of the acidic (type I) subfamily as identified by hybridization-selection of mRNAs, followed by gel electrophoretic identification of the polypeptides synthesized by translation in vitro. The partial amino acid sequence of the amphibian cytokeratin shows strong similarity to type I cytoskeletal keratins from human (mol. wt. 50 000) and murine (mol. wt. 59 000) epidermis. In the non alpha-helical tail region the human and the non-mammalian (Xenopus) keratins are more similar to each other than to the murine protein, indicating that the former are equivalent cytokeratin polypeptides and belonging to a special subclass of type I keratin polypeptides devoid of glycine-rich regions in the carboxy-terminal portion. The evolutionary conservativity of the genes coding for cytokeratins is discussed.

Amino Acid Sequence↗
PubMed1984

Divergent protein coding regions in otherwise closely related androgen-regulated mRNAs.

Rat seminal vesicles serve as a model system for studying androgen action. We have sequenced and compared full length cDNAs for two major proteins (S and F) synthesised and secreted under hormonal control. Overall, mRNAS and mRNAF share 57% nucleotide sequence homology suggesting that their genes arose by duplication of a common ancestor. However, the mRNAs display a highly unusual regional distribution of sequence homology, with the untranslated regions (UTRs) being substantially more homologous than the protein-coding regions (PCRs). Detailed analysis of nucleotide substitutions at synonymous and replacement sites shows that the PCRs have evolved very rapidly. Evolutionary conservation of the UTRs is no higher than that of UTRs generally and thus provides no evidence of a specific regulatory role for the UTRs in androgen action. The primary sequences of proteins S and F have diverged so rapidly that they are the best examples of neutrally evolving proteins for which comparative nucleotide sequence data are available. However, despite their rapid divergence, the predicted higher order structures for both proteins consist largely of non-regular conformation. This is discussed in terms of their roles as structural components of the rodent copulatory plug.

Amino Acid Sequence↗
PubMed1987

Structural models of the redox centres in cytochrome oxidase.

Evolutionary conservation, predicted membrane topography of the subunits, and known chemical and physical properties of the catalytic metals in cytochrome oxidase provided the basis for plausible structural models of the enzyme's redox centres. Subunit II probably binds one of the copper ions (CuA) whilst subunit I is likely to bind the two haems (a and a3) and the other redox-active copper (CuB). Two cysteine and two histidine residues of subunit II are the likely ligands of CuA, forming a centre that may be structurally similar to that in azurin. The two haems may be sandwiched between two transmembranous segments of subunit I, one of which also provides a histidine ligand to CuB. A third segment may provide two more histidine ligands to the latter. The model was constructed with a 4 A Fe-Cu distance in the binuclear haem a3-CuB centre, and a 14 A distance between the haem irons. The subunit I model involves only three transmembranous helices which bind three catalytic metal groups. The fit of this model to several known physicochemical properties of the redox centres is analysed.

Animals↗
PubMed1987

Fungal small nuclear ribonucleoproteins share properties with plant and vertebrate U-snRNPs.

snRNAs with properties closely related to those of the major vertebrate U-snRNAs are present in the fungi Aspergillus nidulans, Neurospora crassa and Schizosaccharomyces pombe. These RNAs possess a tri-methyl guanosine cap structure and a subset cross-hybridizes with human U1 and U2 clones. In the form of snRNPs, snRNAs from these fungi as well as from Saccharomyces cerevisiae and pea plants are immunoprecipitated by human and anti-Sm or anti-(U1)RNP autoimmune antibodies. On micro-injection into the cytoplasm of Xenopus oocytes, the snRNAs are packaged into ribonucleoprotein particles and migrate into the nucleus. The results demonstrate a hitherto unsuspected degree of evolutionary conservation in snRNA structure, snRNP protein structure, and sites of RNA-protein interaction within snRNPs.

Animals↗
PubMed1991

Trans splicing integrates an exon of 22 nucleotides into the nad5 mRNA in higher plant mitochondria.

The genes coding for NADH dehydrogenase subunit 5 (nad5) in mitochondria of the higher plants Oenothera and Arabidopsis are split into five exons that are located in three distant genomic regions. These encode exons a + b, c and d + e, respectively. Maturation of the mRNAs requires two trans splicing events to integrate exon c of only 22 nucleotides. Both trans splicing reactions involve mitochondrial group II intron sequences that allow base pairings in the interrupted domain IV, demonstrating the flexibility of intron structures. The observation of fragmented intron sequences in plant mitochondria suggests that trans splicing is more widespread than previously assumed. RNA editing by C to U alterations in both Oenothera and Arabidopsis open reading frames improves the evolutionary conservation of the encoded polypeptides. Three C to U RNA editing events were observed in intron sequences.

Amino Acid Sequence↗
PubMed1994

The Saccharomyces cerevisiae APS1 gene encodes a homolog of the small subunit of the mammalian clathrin AP-1 complex: evidence for functional interaction with clathrin at the Golgi complex.

Clathrin-associated protein (AP) complexes have been implicated in the assembly of clathrin coats and the selectivity of clathrin-mediated protein transport processes. We have identified a yeast gene, APS1, encoding a homolog of the small (referred to herein as sigma) subunits of the mammalian AP-1 complex. Sequence comparisons have shown that Aps1p is more similar to the sigma subunit of the Golgi-localized mammalian AP-1 complex than Aps2p, which is more related to the plasma membrane AP-2 sigma subunit. Like their mammalian counterparts, Aps1p and Aps2p are components of distinct, large (> 200 kDa) complexes and a significant portion of the Aps proteins co-fractionate with clathrin-coated vesicles during gel filtration chromatography. Unexpectedly, even though the evolutionary conservation of AP small subunits is substantial (50% identity between mammalian and yeast proteins), disruptions of APS1 (aps1 delta) and APS2 (aps2 delta), individually or in combination, elicit no detectable mutant phenotypes. These data indicate that the Aps proteins are not absolutely required for clathrin-mediated selective protein transport in cells expressing wild type clathrin. However, aps1 delta accentuated the slow growth and alpha-factor pheromone maturation defect of cells carrying a temperature-sensitive allele of clathrin heavy chain (Chc) (chc1-ts). In contrast, aps1 delta did not influence the effects of chc1-ts on vacuolar protein sorting or receptor-mediated endocytosis. The aps2 delta mutation resulted in a slight effect on chc1-ts cell growth but had no additional effects. The growth defect of cells completely lacking Chc was compounded by aps1 delta but not aps2 delta. These results comprise evidence that Aps1p is involved in a subset of clathrin functions at the Golgi apparatus. The effect of aps1 delta on cells devoid of clathrin function suggests that Aps1p also participates in clathrin-independent processes.

Adaptor Protein Complex 1↗
PubMed1994

Chicken oocyte growth is mediated by an eight ligand binding repeat member of the LDL receptor family.

Deposition of the yolk mass components of chicken oocytes, very low density lipoprotein (VLDL) and vitellogenin (VTG), is mediated by a 95 kDa plasma membrane protein, termed VLDL/VTG receptor (VLDL/VTGR). Molecular characterization of the VLDL/VTGR revealed that it is a member of the LDLR gene superfamily, and harbours eight complement-type, cysteine-rich ligand binding repeats at the N-terminus. This ligand binding domain structure is the hallmark of the recently discovered mammalian so-called VLDLRs, whose true physiological function remains to be elucidated. Northern blot analysis revealed that this receptor is expressed almost exclusively in oocytes, with very much lower levels of hybridizing transcripts present in heart and skeletal muscle. Heterologous expression of the cloned receptor demonstrated its ability to bind both VLDL and VTG. The receptor gene is located on the avian sex chromosome Z, in agreement with the sex linkage of a single-gene defect in animals that fail to reproduce because of the lack of expression of functional VLDL/VTGR. In situ hybridization analysis of oocytes suggested that VLDL/VTGR mRNA may relocalize during oocyte growth. Thus, the current study has identified and characterized the first non-mammalian VLDLR. Its key role in avian reproduction and extremely high evolutionary conservation shed new light on VLDLR function in mammals, which also express the gene in ovaries.

Amino Acid Sequence↗
PubMed2004

WDR26: a novel Gbeta-like protein, suppresses MAPK signaling pathway.

WD40 repeat proteins play important roles in a variety of cellular functions, including cell growth, proliferation, apoptosis, and intracellular signal transduction. Mitogen-activated protein kinases (MAPKs) are evolutionary conserved enzymes in cell signal transduction connecting cell-surface receptors to critical regulatory targets within cells and control cell survival, adaptation, and proliferation. Previous studies revealed that G-protein coupled receptors (GPCRs) play important roles in the signal transduction from extracellular stimuli to MAPKs and the WD40-containing Gbeta proteins as well as Gbeta-like proteins are involved in the stimulation and regulation of the MAPK signaling pathways. Here we report the identification and characterization of a novel human WD40 repeat protein, WD40 repeat protein 26 (WDR26). The cDNA of WDR26 is 3,729 bp, encoding a Gbeta-like protein of 514 amino acids in the cytoplasm. The protein is highly conserved in evolution across different species from yeast, Drosophila, mouse, to human. Northern blot analysis indicates that WDR26 is expressed in most of the examined human tissues, especially at a high level in skeletal muscle. Overexpression of WDR26 in the cell inhibits the transcriptional activities of ETS proteins, ELK-1 and c-fos serum response element (SRE), mediated by MEKK1. These results suggest that WDR26 may act as a negative regulator in MAPK signaling pathway and play an important role in cell signal transduction.

Amino Acid Sequence↗
PubMed2002

Ras family genes: an interesting link between cell cycle and cancer.

Ras genes are evolutionary conserved and codify for a monomeric G protein binding GTP (active form) or GDP (inactive form). The ras genes are ubiquitously expressed although mRNA analysis suggests different level expression in tissue. Mutations in each ras gene frequently were found in different tumors, suggesting their involvement in the development of specific neoplasia. These mutations lead to a constitutive active and potentially oncogenic protein that could cause a deregulation of cell cycle. Ras protein moderates cellular responses at several mitogens and/or differentiation factors and at external stimuli. These stimuli activate a series of signal transduction pathways that either can be independent or interconnected at different points. Recent observations begin to clarify the complex relationship between Ras activation, apoptosis, and cellular proliferation. A greater understanding of these processes would help to identify the factors directly responsible for cell cycle deregulation in several tumors, moreover it would help the design of specific therapeutic strategies, for the control on the proliferation of neoplastic cells. We summarize here current knowledge of ras genes family: structural and functional characteristics of Ras proteins and their links with cell cycle and cancer.

Animals↗