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CEBPA point mutations in hematological malignancies.

The CCAAT/enhancer-binding protein-alpha (CEBPA) is a transcription factor strongly implicated in myelopoiesis through control of proliferation and differentiation of myeloid progenitors. Recently, several works have reported the presence of CEBPA-acquired mutations in hematological malignancies. In this work, we analyzed characteristics of mutations and their correlation with disease characteristics described in previous studies. In the 1175 patients reported, 146 CEBPA mutations were identified in 96 patients. Mutations were found in the whole gene sequence, but cluster regions were clearly identified. Furthermore, two categories of mutations were reported: out-of-frame ins/del often in the N-terminal region, and in-frame ins/del often in the C-terminal region. CEBPA mutations were reported exclusively in acute myeloid leukemia (AML) (according to WHO classification criteria) and mutated patients preferentially belonged to M1, M2 and M4 FAB subtypes. All but one case belonged to the 'intermediate' prognostic subgroup of MRC classification. In the absence of poor prognostic factors, patients with CEBPA mutation had favorable outcome, very similar to that of the t(8;21), inv(16), t(15;17) subgroup. Systematic analysis of CEBPA mutations, in addition to that of alterations in master genes of hematopoiesis, may be useful to assess the prognosis of AML particularly in patients belonging to the 'intermediate' prognostic subgroup.

CCAAT-Enhancer-Binding Protein-alpha↗

Overall deregulation in gene expression as a novel indicator of tumor aggressiveness in colorectal cancer.

Malignant transformation of the cell is accompanied and characterized by disruption of genetic material and aberrant expression of multiple genes. Systematic analysis of differential gene expression in human tumor samples may provide an estimate of the degree of genetic and epigenetic deregulation in neoplastic cells. We have assessed, by means of a RNA differential display technique, the overall gene expression deregulation in a prospectively collected series of 68 human colorectal carcinomas. An index of differential expression has been calculated for each case. A similar proportion of the displayed sequences (23%) was under- and over-represented in the tumor in respect of the normal tissue. An increased variation in the expression profile was observed in advanced Dukes' stages (P < 0.02) and correlated with lymph node invasion (P < 0.05). Furthermore, a diminished overall survival was associated to increased rates of deregulation (Log-rank, P < 0.02) and especially down-regulation (P < 0.001). When Cox multivariate analysis was performed in front of Dukes' stage, both indexes of differential expression were independent indicators of a worse outcome (P = 0.05 and P < 0.01 respectively). We conclude that estimation of the fraction of differentially displayed tags by RNA fingerprinting may have relevant applications in the prognostic assessment of colorectal cancer.

Blotting, Northern↗

Mutant p53 proteins stimulate spontaneous and radiation-induced intrachromosomal homologous recombination independently of the alteration of the transactivation activity and of the G1 checkpoint.

We report here a systematic analysis of the effects of different p53 mutations on both spontaneous and radiation-stimulated homologous recombination in mouse L cells. In order to monitor different recombination pathways, we used both direct and inverted repeat recombination substrates. In each line bearing one of these substrates, we expressed p53 proteins mutated at positions: 175, 248 or 273. p53 mutations leading to an increased spontaneous recombination rate also stimulate radiation-induced recombination. The effect on recombination may be partially related to the conformation of the p53 protein. Moreover, p53 mutations act on recombination between direct repeats as well as between inverted repeats indicating that strand invasion mechanisms are stimulated. Although all of the p53 mutations affect the p53 transactivation activity measured on the WAF1 and MDM2 gene promoters, no correlation between the transactivation activity and the extent of homologous recombination can be drawn. Finally, some p53 mutations do not affect the G1 arrest after radiation but stimulate radiation-induced recombination. These results show that the role of p53 on transactivation and G1 cell cycle checkpoint is separable from its involvement in homologous recombination. A direct participation of p53 in the recombination mechanism itself is discussed.

Animals↗

Aberrant promoter methylation of previously unidentified target genes is a common abnormality in medulloblastomas--implications for tumor biology and potential clinical utility.

Medulloblastomas exhibit an array of diverse cytogenetic abnormalities. To evaluate the significance of epigenetic rather than genetic lesions in medulloblastomas and other primitive neuroectodermal tumors (PNETs) of the childhood CNS we performed a systematic analysis of gene specific and global methylation. Methylation-specific PCR detected no methylation for p15(INK4B), von Hippel Lindau and TP53 and only limited methylation for E-Cadherin and p16(INK4A) in tumors. The cell lines Daoy and MHH-PNET-5 in which the p16(INK4A) promoter was methylated did not express the gene, but demonstrated abnormalities by SSCP. Immunohistochemistry for p16 was negative in all examined normal cerebella and medulloblastomas. Using the technique of Restriction Landmark Genomic Scanning we detected methylation affecting up to 1% of all CpG islands in primary MB/PNETs and 6% in MB cell lines. Methylation patterns differed between medulloblastomas and PNETs. Examination of several methylated sequences revealed homologies to known genes and expressed sequences. Analysis of survival data identified seven of 30 hypermethylated sequences significantly correlating with poor prognosis. We suggest that DNA hypermethylation has an outstanding potential for the identification of novel tumor suppressors as well as diagnostic and therapeutic targets in MBs and other PNETs of the CNS.

Adolescent↗

hH-Rev107, a class II tumor suppressor gene, is expressed by post-meiotic testicular germ cells and CIS cells but not by human testicular germ cell tumors.

By systematic analysis of a human testis library, we have isolated the hH-Rev107-3 cDNA, identical to hH-Rev107-1 cDNA, which was previously described as a class II tumor suppressor gene. In this study, two transcripts (1 and 0.8 kb) were detected by Northern blot in all human tissues, excepted in thymus. The strongest expression was found in testis, skeletal muscle and heart. These two mRNA are probably transcribed from only one gene that we mapped to the q12-q13 region of the chromosome 11. In human testis, hH-Rev107 gene expression was localized, by in situ hybridization, within the round spermatids. To investigate a possible role for hH-Rev107 protein in testicular malignant growth, we examined the expression of this gene in germ cell tumors. A strong hH-Rev107 gene expression was observed in normal testis as well as in samples with preinvasive carcinoma in situ but was completely absent in overt tumors, both seminomas and non-seminomas. By in situ hybridization, CIS was found hH-Rev107 positive and tumor negative. A semi-quantitative assessment of hH-Rev107 mRNA level in testicular germ cell tumors, by RT-PCR, exhibited a ninefold decrease in the gene expression. No gross structural aberrations of hH-Rev107 gene were detected in these human primary tumors. The results suggest that down-regulation of hH-Rev107 may be associated with invasive progression of testicular germ cell tumors.

Amino Acid Sequence↗

Genomic instability and cancer: scanning the Caenorhabditis elegans genome for tumor suppressors.

Maintaining the stability of the genome is critical to normal cell growth and development. The early notion that cancer is the result of mutations in genes controlling cellular growth implied that gene or genome integrity is vital to the prevention of oncogenesis, and many genes and pathways that prevent genomic deterioration have been identified over the past decades. Recent progress in reverse genetic approaches, principally RNA interference, now allows the systematic analysis of gene function on a genomic scale in an animal system. Here, we discuss genomic approaches in the model organism Caenorhabditis elegans, aimed to identify genes and genetic networks that contribute to genome stability and are thus potentially involved in human carcinogenesis.

Animals↗

dapk1, encoding an activator of a p19ARF-p53-mediated apoptotic checkpoint, is a transcription target of p53.

The p53 tumour suppressor functions as a transcriptional activator, and several p53-inducible genes that play a critical proapoptotic role have been described. Moreover, p53 regulates the expression of various proteins participating in autoregulatory feedback loops, including proteins that negatively control p53 stability (Mdm2 and Pirh2) or modulate stress-induced phosphorylation of p53 on Ser-46 (p53DINP1 or Wip1), a key event for p53-induced apoptosis. Here, we describe a new systematic analysis of p53 targets using oligonucleotide chips, and report the identification of dapk1 as a novel p53 target. We demonstrate that dapk1 mRNA levels increase in a p53-dependent manner in various cellular settings. Both human and mouse dapk1 genomic loci contain DNA sequences that bind p53 in vitro and in vivo. Since dapk1 encodes a serine/threonine kinase previously shown to suppress oncogene-induced transformation by activating a p19ARF/p53-dependent apoptotic checkpoint, our results suggest that Dapk1 participates in a new positive feedback loop controlling p53 activation and apoptosis.

Animals↗

Selective recognition of inositol phosphates by subtypes of the inositol trisphosphate receptor.

Synthetic analogues of inositol trisphosphate (IP(3)), all of which included structures equivalent to the 4,5-bisphosphate of (1,4,5)IP(3), were used to probe the recognition properties of rat full-length type 1, 2 and 3 IP(3) receptors expressed in insect Spodoptera frugiperda 9 cells. Using equilibrium competition binding with [(3)H](1,4,5)IP(3) in Ca(2+)-free cytosol-like medium, the relative affinities of the receptor subtypes for (1,4,5)IP(3) were type 3 (K(d)=11+/-2 nM)>type 2 (K(d)=17+/-2 nM)>type 1 (K(d)=24+/-4 nM). (1,4,5)IP(3) binding was reversibly stimulated by increased pH, but the subtypes differed in their sensitivity to pH (type 1>type 2>type 3). For all three subtypes, the equatorial 6-hydroxy group of (1,4,5)IP(3) was essential for high-affinity binding, the equatorial 3-hydroxy group significantly improved affinity, and the axial 2-hydroxy group was insignificant; a 1-phosphate (or in its absence, a 2-phosphate) improved binding affinity. The subtypes differed in the extents to which they tolerated inversion of the 3-hydroxy group of (1,4,5)IP(3) (type 1>type 2>type 3), and this probably accounts for the selectivity of (1,4,6)IP(3) for type 1 receptors. They also differed in their tolerance of inversion, removal or substitution (by phosphate) of the 2-hydroxy group (types 2 and 3>type 1), hence the selectivity of (1,2,4,5)IP(4) for type 2 and 3 receptors. Removal of the 3-hydroxy group or its replacement by fluorine or CH(2)OH was best tolerated by type 3 receptors, and accounts for the selectivity of 3-deoxy(1,4,5)IP(3) for type 3 receptors. Our results provide the first systematic analysis of the recognition properties of IP(3) receptor subtypes and have identified the 2- and 3-positions of (1,4,5)IP(3) as key determinants of subtype selectivity.

Amino Acid Sequence↗

Signalling activity of beta-catenin targeted to different subcellular compartments.

Beta-catenin plays a dual role as an adhesion molecule in adherens junctions at the plasma membrane and as a key intermediate in the canonical Wnt signalling pathway. The cytosolic soluble pool of beta-catenin, involved in the transmission of the Wnt signal, is normally subjected to rapid protein degradation. On activation of the Wnt cascade, beta-catenin becomes stabilized and then translocates into the nucleus where it co-activates transcription factors of the TCF (T-cell factor)/LEF (lymphoid enhancer factor) family. The expression of plasma membrane-targeted forms of beta-catenin has been shown to also activate TCF/LEF-dependent transcription and different mechanisms have been put forward. In the present study, we have undertaken a systematic analysis of the signalling capability of non-degradable forms of beta-catenin targeted to different cellular compartments. beta-Catenin targeted to the plasma membrane activated transcription to a greater extent compared with non-targeted beta-catenin, and led to a marked stabilization of cytosolic soluble beta-catenin. These effects were independent of the competition with endogenous beta-catenin for binding to E-cadherin at the plasma membrane, since targeting non-degradable beta-catenin to other cellular compartments, i.e. the outer mitochondrial membrane and the endoplasmic reticulum membrane, also resulted in the accumulation of cytosolic wild-type beta-catenin and activation of beta-catenin-dependent signalling. In contrast, nuclear-targeted beta-catenin was without significant effect on cytosolic wild-type beta-catenin and did not activate transcription. Our results suggest that cytosolic accumulation of beta-catenin is a prerequisite for the activation of TCF/LEF-dependent transcription in the nucleus.

Cadherins↗

Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4.

The genome of bacteriophage T4 encodes three polynucleotide ligases, which seal the backbone of nucleic acids during infection of host bacteria. The T4Dnl (T4 DNA ligase) and two RNA ligases [T4Rnl1 (T4 RNA ligase 1) and T4Rnl2] join a diverse array of substrates, including nicks that are present in double-stranded nucleic acids, albeit with different efficiencies. To unravel the biochemical and functional relationship between these proteins, a systematic analysis of their substrate specificity was performed using recombinant proteins. The ability of each protein to ligate 20 bp double-stranded oligonucleotides containing a single-strand break was determined. Between 4 and 37 degrees C, all proteins ligated substrates containing various combinations of DNA and RNA. The RNA ligases ligated a more diverse set of substrates than T4Dnl and, generally, T4Rnl1 had 50-1000-fold lower activity than T4Rnl2. In assays using identical conditions, optimal ligation of all substrates was at pH 8 for T4Dnl and T4Rnl1 and pH 7 for T4Rnl2, demonstrating that the protein dictates the pH optimum for ligation. All proteins ligated a substrate containing DNA as the unbroken strand, with the nucleotides at the nick of the broken strand being RNA at the 3'-hydroxy group and DNA at the 5'-phosphate. Since this RNA-DNA hybrid was joined at a similar maximal rate by T4Dnl and T4Rnl2 at 37 degrees C, we consider the possibility that this could be an unexpected physiological substrate used during some pathways of 'DNA repair'.

Bacteriophage T4↗

Structural features that make oligopeptides susceptible substrates for hydrolysis by recombinant thimet oligopeptidase.

A systematic analysis of the peptide sequences and lengths of several homologues of bioactive peptides and of a number of quenched-fluorescence (qf) opioid- and bradykinin-related peptides was performed to determine the main features leading the oligopeptides to hydrolysis by the recombinant rat testis thimet oligopeptidase (EC 3.4.24.15). The results indicate that a minimum substrate length of six amino acids is required and that among the oligopeptides six to thirteen amino acid residues long, their susceptibility as substrates is highly variable. Thimet oligopeptidase was able to hydrolyse, with similar catalytic efficiency, peptide bonds having hydrophobic or hydrophilic amino acids as well as proline in the P1 position of peptides, ranging from a minimum of six to a maximum of approximately thirteen amino acid residues. An intriguing observation was the shift of the cleavage site, at a Leu-Arg bond in qf dynorphin-(2-8) [qf-Dyn2-8; Abz-GGFLRRV-EDDnp, where Abz stands for o-aminobenzoyl and EDDnp for N-(2,4-dinitrophenyl)ethylenediamine], to Arg-Arg in qf-Dyn2-8Q, in which Gln was substituted for Val at its C-terminus. Similarly, a cleavage site displacement was also observed with the hydrolysis of the internally quenched-fluorescence bradykinin analogues containing Gln at the C-terminal position, namely Abz-RPPGFSPFR-EDDnp and Abz-GFSPFR-EDDnp are cleaved at the Phe-Ser bond, but Abz-RPPGFSPFRQ-EDDnp and Abz-GFSPFRQ-EDDnp are cleaved at the Pro-Phe bond.

Amino Acid Sequence↗

Molecular cloning and functional expression of a novel human gene encoding two 41-43 kDa skeletal muscle internal membrane proteins.

Systematic analysis of gene transcript repertoires prepared from libraries made with various specific human tissues permitted isolation of many partially sequenced cDNA clones. A few of these represented novel genes with limited or no similarity to known genes from humans or other species. The present study set out to isolate and sequence the full-length cDNA corresponding to one of these novel human transcripts, and identify the corresponding protein product at the subcellular level. Current sequence analyses have revealed that the protein contains a hydrophobic N-terminal segment and an internal leucine-zipper motif. Numerous sites of putative post-translational modifications, such as N-linked glycosylation, myristoylation and phosphorylation sites, were also identified. Using one monoclonal antibody raised against a recombinant fragment, two different 41-43 kDa proteins were detected in human skeletal muscle, heart and placenta homogenates at various ratios. Both immunodetected protein products of the novel human gene were distributed in the transverse tubules and/or near the junctional sarcoplasmic reticulum within skeletal muscle cells. Both proteins had physical properties believed to be attributable to integral membrane components. Finally, the GENX-3414 gene was chromosomally localized at position 4q24-q25.

Adult↗

Eukaryotic Fe-hydrogenases -- old eukaryotic heritage or adaptive acquisitions?

All eukaryotes seem to possess proteins that most probably evolved from an ancestral Fe-hydrogenase. These proteins, known as NARF or Nar, do not produce hydrogen. Notably, a small group of rather unrelated unicellular anaerobes and a few algae possess Fe-hydrogenases, which produce hydrogen. In most, but not all organisms, hydrogen production occurs in membrane-bounded organelles, i.e. hydrogenosomes or plastids. Whereas plastids are monophyletic, hydrogenosomes evolved repeatedly and independently from mitochondria or mitochondria-like organelles. A systematic analysis of the various hydrogenosomes and their hydrogenases will contribute to an understanding of the evolution of the eukaryotic cell, and provide clues to the evolutionary origin(s) of the Fe-hydrogenase.

Eukaryotic Cells↗

Sample size effects on temporal reliability of language sample measures of preschool children.

The present study examined the temporal reliability of four quantitative measurements of operationally defined linguistic behaviors observed in a naturalistic setting. The measures of language production were computed using the Systematic Analysis of Language Transcripts (SALT) software from two 20-minute language samples obtained 3 to 14 days apart for each of 20 preschool-aged children. Samples were edited to different sizes based either on duration (12 or 20 minutes) or on limits of the total number of complete and intelligible utterances (from 25 to 175 in increments of 25). Inadequate reliability was found for the language sample measure, total number of words; hence, the validity of this measure is questionable. In contrast, very high temporal reliability coefficients (r > .92) were obtained for the language sample measures of number of different words, mean length of utterance in morphemes, and mean sentence length in morphemes when derived from a large number (> or = 175) of complete and intelligible utterances. The temporal reliability of these measures reached acceptable levels, not only for research purposes, but for diagnostic purposes as well.

Child, Preschool↗

Platelet alpha2-adrenoceptor alterations in patients with essential hypertension.

AIMS: The purpose of this study was to determine whether human platelet alpha2-adrenoceptors were altered in essential hypertension. A systematic analysis was carried out on 165 normotensives and 124 untreated primary hypertensives. METHODS: The study was performed at different levels: i) density and affinity of platelet alpha2-adrenoceptors were determined by receptor binding assays using the full alpha2-adrenoceptor agonist [3H]-UK 14304 and a thermodynamic analysis of data was carried out to evaluate if binding mechanisms at the molecular level were altered during hypertension; ii) the functionality of Gi proteins coupled to alpha2-adrenoceptors and iii) forskolin-stimulated cAMP levels were measured. RESULTS: Platelet alpha2-adrenoceptors mean density (Bmax) and affinity (Kd) (+/-s.e.mean) were significantly lower and higher, respectively, in normotensive than in hypertensive subjects [Bmax=327+/-4 vs 435+/-5 fmol mg(-1) of protein (P<0.01) and Kd=3.76+/-10.05 vs 6.50+/-0.15 nM (P<0.01), respectively]. The 50% stimulating concentration of adrenaline on [35S]-GTPgammaS binding to Gi proteins was significantly (P<0.01) lower in normotensives (12+/-2 nM) than in hypertensives (110+/-10 nM). The 50% inhibiting concentration of adrenaline on forskolin-stimulated cAMP levels was significantly (P<0.01) lower in normotensive (22+/-2 nM) than in hypertensive subjects (200+/-25 nM). CONCLUSIONS: Present analysis, including receptorial and functional data, provides evidence that marked alterations occur in platelet alpha2-adrenoceptors of hypertensive subjects.

Adrenergic alpha-Antagonists↗

Prenatal ontogeny of lymphocyte subpopulations in pigs.

Although porcine lymphocytes have been classified into numerous subpopulations in postnatal animals, little is known about the ontogeny of these complex cell subsets. Using double- and triple-colour flow cytometry (FCM), we investigated the surface phenotype of fetal lymphoid cells in the thymus, cord blood, spleen and mesenteric lymph nodes at different stages of gestation. It was found that the major lymphocyte subpopulations started to appear at the beginning of the second third of the gestation period, with B cells being the earliest lymphocyte subpopulation to appear in the periphery. The T-cell receptor (TCR) gamma delta+ cells were the earliest detectable T-cell subset, developing first in the thymus and subsequently arriving in the periphery. Later in ontogeny, however, the number of TCRalpha beta+ lymphocytes rapidly increased, becoming the predominant T cells both in the thymus and in the periphery. Cells with the phenotype of adult natural killer cells were also identified in pig fetuses, though their nature and functional roles remain to be investigated. In addition, CD2 was expressed on most B cells whilst very few CD4+ TCRalpha beta+ cells or CD2+ TCRgamma delta+ cells expressed CD8, suggesting that the expression of CD2 and CD8 may reflect the functional status of the cells in postnatal animals. Taken together, this study has provided a systematic analysis of fetal porcine lymphocyte subpopulations and may provide the base for studies to establish the physiological roles of these lymphocyte subsets.

Animals↗

Evaluation of reflective learning in a psychodynamic group of nurses caring for terminally ill patients.

The development of a psychodynamic group comprising seven female nurses was studied for 1 year (31 sessions). The group was part of a 1-year postgraduate training in patient-centred nursing. The members of the group all worked on the same unit; none of them left the unit or the group during the study. As the nurse-patient relationship is considered to be crucial for patient-centred nursing, the group sessions focused on the problems which the nurses experienced in their relationships with the patients. The objective of the group-work was to improve the nurses' ability to reflect on these relationships. The purpose of the study was to evaluate the group sessions, concentrating on the characteristics of patients selected for discussions, group process over time, and impact of specific patient characteristics on the group-work. Transcriptions of the tape-recorded group sessions were made for systematic analysis. A category system was developed and validated to rate reflection about the patient, the nurses themselves and the nurse-patient relationship. The results showed that the nurses over-proportionally selected terminally ill patients, as well as patients who were female and within a similar age range as themselves. These results could be due to an identification with these patients, causing increased psychological stress on the nurses. Throughout the year, the nurses' verbal activity and their reflections about their patients increased, whereas their reflections about themselves decreased. The need to withdraw and protect oneself by focusing more on the patient than on oneself might have been a strategy the nurses used to cope with growing stress.

Adult↗

Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo.

In a genetic selection designed to isolate Escherichia coli mutations that increase expression of the IS 10 transposase gene (tnp), we unexpectedly obtained viable mutants defective in translation initiation factor 3 (IF3). Several lines of evidence led us to conclude that transposase expression, per se, was not increased. Rather, these mutations appear to increase expression of the tnp'-'lacZ gene fusions used in this screen, by increasing translation initiation at downstream, atypical initiation codons. To test this hypothesis we undertook a systematic analysis of start codon requirements and measured the effects of IF3 mutations on initiation from various start codons. Beginning with an efficient translation initiation site, we varied the AUG start codon to all possible codons that differed from AUG by one nucleotide. These potential start codons fall into distinct classes with regard to translation efficiency in vivo: Class I codons (AUG, GUG, and UUG) support efficient translation; Class IIA codons (CUG, AUU, AUC, AUA, and ACG) support translation at levels only 1-3% that of AUG; and Class IIB codons (AGG and AAG) permit levels of translation too low for reliable quantification, importantly, the IF3 mutations had no effect on translation from Class I codons, but they increased translation from Class II codons 3-5-fold, and this same effect was seen in other gene contexts. Therefore, IF3 is generally able to discriminate between efficient and inefficient codons in vivo, consistent with earlier in vitro observations. We discuss these observations as they relate to IF3 autoregulation and the mechanism of IF3 function.

Bacterial Proteins↗