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Eukaryotic initiation factor 5A-1 (eIF5A-1) as a diagnostic marker for aberrant proliferation in intraepithelial neoplasia of the vulva.

OBJECTIVE: The mature eukaryotic translation initiation factor 5A contains the unusual amino acid hypusine, formed post-translationally from a specific lysine residue and essential for proliferation of eukaryotic cells. We hypothesized that the major eIF5A isoform, eIF5A-1, is an in situ biomarker for proliferation. NIH-353, a polyclonal immunoreagent specific for hypusine-containing eIF5A-1, was used to test this proposal in biopsies of vulvar high-grade intraepithelial neoplasia (VIN), characterized by the presence of proliferating cells throughout the thickness of the epithelium. Methods. Formalin-fixed and paraffin-embedded archival samples with an independently established diagnosis of VIN 3 were stained immunohistochemically after antigen retrieval, employing NIH-353 and, for comparison, the standard Ki-67 antibody. RESULTS: NIH-353 labeled neoplastic keratinocytes throughout the thickness of the epithelium in all VIN 3 samples. Malignant cells in a case of focally invasive squamous cell carcinoma also stained strongly for mature, hypusine-containing eIF5A-1. Epithelium adjacent to these lesions, though still of apparently normal morphology, was immunoreactive throughout its full thickness. At inflammatory foci of lesional sites, solitary reactive lymphocytes were positive, as were individual proliferating cells within dermal appendages. The submucosal stroma lacked reactive cells. CONCLUSION: NIH-353 identifies mature eIF5A-1 as an in situ biomarker for proliferation. Like Ki-67, this immunoreagent promises broad applicability in histopathological diagnosis and may be helpful in outcome prediction. In contrast to Ki-67, NIH-353 visualizes a molecular target for antineoplastic therapy, and thus may guide the development and clinical testing of drugs that, like the fungicide ciclopirox, inhibit hypusine formation and cell proliferation.

Animals↗

[Expression of MOST-1 mRNA in bone marrow mononuclear cells from patients with acute lymphoblastic leukemia].

OBJECTIVE: To investigate the MOST-1 mRNA expression in bone marrow (BM) mononuclear cells in children with acute lymphoblastic leukemia, and to explore its association with immunophenotype and treatment response. METHODS: Semiquantitative RT-PCR was employed to study the MOST-1 mRNA expression in BM mononuclear cells separated by Ficoll density gradient method. The MOST-1 expression levels were represented by the ratio of MOST-1 band pixels against its corresponding housekeeping gene beta-actin mRNA band pixels determined by GDS8000 densitometry and GelWork-1 analysis software. The PCR product was eluted and sequenced, and its sequence was confirmed by Pairwise BLAST search. RESULTS: A total of 17 children with acute lymphoblastic leukemia were studied. MOST-1 mRNA was exclusively expressed in the mononuclear cells from 3 patients with ALL-L3 type. However, there was no MOST-1 mRNA expression in other 14 children with ALL-L1 or ALL-L2, irrespective of their initial peripheral WBC count and blast cell percentage in peripheral blood and bone marrow. The MOST-1 mRNA expression levels in two of the ALL-L3 patients with higher blast cell percentages in peripheral blood and bone marrow were 3- and 2-fold respectively as compared with that in the third ALL-L3 child with lower initial blast cell load. MOST-1 mRNA expression was no longer detected in the two ALL-L3 children after complete remission with combination chemotherapy. CONCLUSION: MOST-1 was expressed in the bone marrow mononuclear cells in patients with ALL-L3, and its expression level was somewhat related to tumor cell burden. It might be implicated in the leukemogenesis of ALL-L3 and might serve as an indicator of tumor burden and thus a useful guide for clinical management.

Bone Marrow Cells↗

Human development IV: the living cell has information-directed self-organisation.

In this paper, restricted to describe the ontogenesis of the cell, we discuss the processing of DNA through RNA to proteins and argue that this process is not able to transfer the information necessary to organize the proteins in the cell, but only to transfer the information necessary to form the shape of the proteins. We shortly describe the structure of the information carrying field recruited by the cells that we think is responsible for building the organelles and other cellular structures. We use the cells superior control of its cytoskeleton as an example of how the cell is using an informational field giving the positional information guiding all the local chemical processes behind the cell movement. We describe the information-directed self-organization in cells and argue that this can explain the ontogenesis of the cell. We also suggest the existence of an undiscovered phenomenon behind the information transmitting cell interactions. We conclude that during evolution the cell has developed into an information-guided self-organizing structure. The mystery we want to solve is: what is the mechanical cause and nature of biological information?

Animals↗

Anatomy of rat semaphorin III/collapsin-1 mRNA expression and relationship to developing nerve tracts during neuroembryogenesis.

Semaphorin III/collapsin-1 (semaIII/coll-1) is a chemorepellent that exhibits a repulsive effect on growth cones of dorsal root ganglion neurons. To identify structures that express semaIII/coll-1 in developing mammals, we cloned the rat homologue and performed in situ hybridization on embryonic, neonatal, and adult rats. The relationship between semaIII/coll-1 mRNA distribution and developing nerve tracts was studied by combining in situ hybridization with immunohistochemistry for markers of growing nerve fibers. At embryonic day 11, semaIII/coll-1 expression was restricted to the olfactory pit, the basal and rostral surface of the telencephalic vesicle, the anlage of the eye, the epithelium of Rathke's pouch, and the somites. At later developmental stages, semaIII/coll-1 mRNA was found to be widely distributed in neuronal as well as in mesenchymal and epithelial structures outside the nervous system. Strong expression was found in the olfactory bulb, retina, lens, piriform cortex, amygdalostriatal area, pons, cerebellar anlage, motor nuclei of cranial nerves, and ventral spinal cord. After birth, mesenchymal staining decreased rapidly and expression became progressively restricted to specific sets of neurons in the central nervous system (CNS). In the mature CNS, semaIII/coll-1 mRNA remains detectable in mitral cells, neurons of the accessory bulb and cerebral cortex, cerebellar Purkinje cells, as well as a subset of cranial and spinal motoneurons. The temporal and spatial expression pattern of semaIII/coll-1 mRNA and its relationship to emerging nerve tracts suggests that semaIII/coll-1 is involved in guiding growing axons towards their targets by forming a molecular boundary that instructs axons to engage in the formation of specific nerve tracts.

Animals↗

Drug development for ovarian hyper-stimulation and anti-cancer treatment: blocking of gonadotropin signaling for epiregulin and amphiregulin biosynthesis.

Gonadotropins play a crucial role in ovarian homeostasis and fertilization through the activation of the cAMP cascade. However, gonadotropin hyper-stimulation may be associated with higher risk for ovarian cancer development. It has been suggested, that high gonadotropin levels in peritoneal and ovarian cystic fluids of patients suffering from benign ovarian cysts, may lead to malignancy. Moreover, we have recently discovered that gonadotropin stimulation can activate the MAPK cascade in target cells. Using DNA microarray technology and RNA from human granulosa cells, we discovered that stimulation with saturating doses of gonadotropins dramatically elevates activity of genes coding for epiregulin and amphiregulin. These gene products can bind and activate the EGF receptor and ERBB4, which are associated with the development of various cancers such as ovarian, breast endometrial and other non-gynecological malignancies. Gonadotropin receptors are expressed not only in the gonads, but also in non-gonadal tissues and in cancer cells. The discovery that gonadotropins activate certain mitogenic signal transduction pathways, may serve as a guide for novel anti-cancer therapy by (1) specific interference at the receptor level to block the gonadotropic response, or arresting the receptor expression and (2) blocking downstream mitogenic signals generated by these hormones, like attenuation of the expression of epiregulin and amphiregulin that belong to the EGF family, using anti-sense and/or SiRNA techniques targeted to suppress their expression. Moreover, since amphiregulin and epiregulin act as mediators of luteinizing hormone (LH) action in the mammalian ovulatory follicles, regulation of the expression of these factors may open new possibilities in treatment of ovarian malfunction implicated with ovarian hyper-stimulation.

Amphiregulin↗

RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus.

The Dlk1-Gtl2 imprinted domain, encompassing the callipyge (CLPG) locus in sheep, has recently been shown to harbor a large number of maternally expressed miRNA genes [1, 2]. Two of these (mir127 and mir136) are processed from a transcript (antiPeg11) that is antisense to Rtl1/Peg11, a paternally expressed intronless gene with homology to the gag and pol polyproteins of Sushi-like retroelements [3]. We herein demonstrate that several additional miRNAs are processed from antiPeg11 and that these regulate Rtl1/Peg11 in trans by guiding RISC-mediated cleavage of its mRNA. This is the first demonstration of miRNA-mediated RNAi involving imprinted genes in mammals.

Animals↗

Enhanced glial activation and expression of specific CNS inflammation-related molecules in aged versus young rats following cortical stab injury.

Aging is associated with increased glial responsiveness that may enhance the brain's susceptibility to injury and disease. To determine whether unique age-related molecular responses occur in brain injury, we assessed mRNA levels of representative central nervous system (CNS) inflammation-related molecules in young (3 months) and aged (36 months) Fisher 344/Brown Norwegian F1 hybrid rats following cortical stab. Enhanced glial activation in older animals was accompanied by increased expression of a subset of inflammation-related mRNAs, including IL-1beta, TNFalpha, IL-6, ICAM-1, inducible nitric oxide synthase (iNOS), metalloproteinase-9 (MMP-9), and complement 3alpha-chain 1 (C3alpha1). Recognition of these age-specific differences may guide development of novel treatment regimes for older individuals.

Aging↗

Comprehensive genetic selection revealed essential bases in the peptidyl-transferase center.

During protein synthesis, the ribosome catalyzes peptide-bond formation. Biochemical and structural studies revealed that conserved nucleotides in the peptidyl-transferase center (PTC) and its proximity may play a key role in peptide-bond formation; the exact mechanism involved remains unclear. To more precisely define the functional importance of the highly conserved residues, we used a systematic genetic method, which we named SSER (systematic selection of functional sequences by enforced replacement), that allowed us to identify essential nucleotides for ribosomal function from randomized rRNA libraries in Escherichia coli cells. These libraries were constructed by complete randomization of the critical regions in and around the PTC. The selected variants contained natural rRNA sequences from other organisms and organelles as well as unnatural functional sequences; hence providing insights into the functional roles played by these essential bases and suggesting how the universal catalytic mechanism of peptide-bond formation could evolve in all living organisms. Our results highlight essential bases and interactions, which are shaping the PTC architecture and guiding the motions of the tRNA terminus from the A to the P site, found to be crucial not only for the formation of the peptide bond but also for nascent chain elongation.

Base Sequence↗

A gene expression map of the Arabidopsis root.

A global map of gene expression within an organ can identify genes with coordinated expression in localized domains, thereby relating gene activity to cell fate and tissue specialization. Here, we present localization of expression of more than 22,000 genes in the Arabidopsis root. Gene expression was mapped to 15 different zones of the root that correspond to cell types and tissues at progressive developmental stages. Patterns of gene expression traverse traditional anatomical boundaries and show cassettes of hormonal response. Chromosomal clustering defined some coregulated genes. This expression map correlates groups of genes to specific cell fates and should serve to guide reverse genetics.

Arabidopsis↗

Functional characterization of 2'-O-methylation and pseudouridylation guide RNAs.

Pseudouridines and 2'-O-methylated nucleotides are ubiquitous constituents of stable cellular RNAs. In eukaryotes, posttranscriptional synthesis of most pseudouridines and 2'-O-methylated nucleotides is directed by sequence-specific guide RNAs (gRNAs). In recent years, an enormous number of novel putative modification gRNAs have been identified in a broad variety of organisms by using bioinformatics and large-scale cDNA-sequencing approaches. Understanding of the function of the novel modification gRNAs as well as the functional importance of modified nucleotides requires techniques that support the site-specific detection of 2'-O-methylated nucleotides and pseudouridines. Here, we describe rapid, reverse transcription-based methods to map 2'-O-methylated nucleotides and pseudouridines in any cellular RNA.

DNA Primers↗

[Expression of BMP-2, TGF-beta, bFGF in guided bone regeneration].

OBJECTIVE: To study the mechanism of guided bone regeneration combined with osteoinduction by observation of expression of BMP-2, TGF-beta, bFGF. METHODS: 42 adult, male, New Zealand rabbits were randomly divided into 6 groups, each group being 7 rabbits. 10mm standard bone defect model was produced bilaterally in the middle radial shaft of each rabbit. Randomly, one defect enveloped with silicon membrane was tested, and the other served as control, sacrificed at 3 days, 1, 2, 3, 4, 5 weeks after surgery for histological observation, immunohistochemical staining of BMP-2, TGF-beta, bFGF and in situ hybridization of their cDNA probes. RESULTS: Histologically bone defects was sealed by silicon membrane, in which inflammation tissue and callus were formed from cells in bone ends. Similar expression of BMP-2, TGF-beta, bFGF between the test groups and control groups was noted. Inflammatory cells in the hematoma expressed bFGF and proliferating periosteal cells, endosteal cells, medullary mesenchymal cells expressed TGF-beta at 3 days postoperatively. Osteocytes in the bone ends and osteoblasts lining callus surface started to express BMP-2, TGF-beta at first week after surgery. Following the formation of inflammation tissue, in which giant cells, macrophages, mesenchymal cells expressed TGF-beta, bFGF respectively. Although the expression of three osteoinductors was the same between the test and control sides, their content was very different in both sides. The whole content in all test sides was much more than all control sides (P < 0.01), the content of test side was also much more than control side in each group. CONCLUSIONS: It is a key reason for successful guided bone regeneration that membrane tube formed a relatively independent bone regenerative situation to prevent around tissue from interruption, and to prevent osteoinductors from diffusion, so that enhanced osteoinductors induced bone regeneration to repair bone defects.

Animals↗

[Input and output channels of quantum biocomputers].

It is proposed that "Quantum Molecular" computer of a neuron consists of the cell cytoskeleton serving as calculating media and input ionic channel sending a hypersound signal to observe these media. The sound spreads through the media travelling along microtubules and microfilaments and switching between those via molecular bridges which serve as elementary switches. The whole system works like a wave guiding net connecting input ionic channels (which generate different sound signals) and output ionic channels (which are controlled by the processed sound signals). Thus the output of such systems depends on the input (controlled by synaptic activity) and on the construction and state of these calculating media. We think that the sound waves spreading through different calculating media solve different physical problems. The construction of the calculating part of the cytoskeleton, according to the hypothesis, is different in different neurons. It is defined by special protein which is produced by DNA, RNA and protein molecular word processor (during brain development and, may be, education). We comment on how the existence of an extremal computer produces an impact on physics and mathematics exemplified by the optimality principle as substitution of physical relativity principle for a complex problem.

Brain↗

Effect of microwaves (2450-MHz) on the immune system in mice: studies of nucleic acid and protein synthesis.

CBA/J adult male mice were given single or triple exposures to 2450-mHz microwaves in an environmentally controlled wave guide facility. The average absorbed dose rate for a single exposure varied from 12 to 15 mW/g. Sham-exposed mice served as controls. Lymphoid cells were collected and tested for metabolic activity on days 3, 6, and 9 following a single exposure, and on days 9, 12, and 16 following triple exposures on days 0, 3, and 6. Cells were cultured in vitro for four hours to seven days before their metabolic rates were assayed. Under these conditions, microwaves failed to produce any detectable change in deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein synthesis, as measured by the incorporation of methyl(3H)-thymidine (3H-TDR) (DNA substrate), 3H-uridine (3H-UR) (RNA substrate), and 3H-leucine (protein substrate) by spleen, bone marrow, and peripheral blood lymphocytes (PBL) in vitro. These data suggest that microwave-induced increases in the frequency of complement-receptor (CR)- or surface-immunoglobulin (sIg)-bearing cells were not associated with a concomitant increase in cell proliferation and/or protein synthesis, and favor the concept that microwaves under these conditions stimulate already existing B-cell precursors for maturation.

Animals↗

Low-density lipoprotein receptor--its structure, function, and mutations.

Uptake of cholesterol, mediated by the low-density lipoprotein (LDL)-receptor, plays a crucial role in lipoprotein metabolism. The LDL-receptor is responsible for the binding and subsequent cellular uptake of apolipoprotein B- and E-containing lipoproteins. To accomplish this, the receptor has to be transported from the site of synthesis, the membranes of the rough endoplasmatic reticulum (ER), through the Golgi apparatus, to its position on the surface of the cellular membrane. The translation of LDL-receptor messenger RNA into the polypeptide chain for the receptor protein takes place on the surface-bound ribosomes of the rough ER. Immature O-linked carbohydrate chains are attached to this integral precursor membrane protein. The molecular weight of the receptor at this stage is 120.000 d. The precursor-protein is transported from the rough ER to the Golgi apparatus, where the O-linked sugar chains are elongated until their final size is reached. The molecular weight has then increased to 160.000 d. The mature LDL-receptor is subsequently guided to the "coated pits" on the cell surface. These specialized areas of the cell membrane are rich in clathrin and interact with the LDL-receptor protein. Only here can the LDL-receptor bind LDL-particles. Within 3 to 5 minutes of its formation, the LDL-particle-receptor complex is internalized through endocytosis and is further metabolized through the receptor-mediated endocytosis pathway. Mutations in the gene coding for the LDL-receptor can interfere to a varying extent with all the different stages of the posttranslational processing, binding, uptake, and subsequent dissociation of the LDL-particle-LDL-receptor complex, but invariably the mutations lead to familial hypercholesterolemia. Thus, mutations in the LDL-receptor gene give rise to a substantially varying clinical expression of familial hypercholesterolemia.

Genotype↗

Different signaling pathways in the livers of patients with chronic hepatitis B or chronic hepatitis C.

The clinical manifestations of chronic hepatitis B (CH-B) and chronic hepatitis C (CH-C) are different. We previously reported differences in the gene expression profiles of liver tissue infected with CH-B or CH-C; however, the signaling pathways underlying each condition have yet to be clarified. Using a newly constructed cDNA microarray consisting of 9614 clones selected from 256,550 tags of hepatic serial analysis of gene expression (SAGE) libraries, we compared the gene expression profiles of liver tissue from 24 CH-B patients with those of 23 CH-C patients. Laser capture microdissection was used to isolate hepatocytes from liver lobules and infiltrating lymphoid cells from the portal area, from 16 patients, for gene expression analysis. Furthermore, the comprehensive gene network was analyzed using SAGE libraries of CH-B and CH-C. Supervised and nonsupervised learning methods revealed that gene expression was correlated more with the infecting virus than any other clinical parameters such as histological stage and disease activity. Pro-apoptotic and DNA repair responses were predominant in CH-B with p53 and 14-3-3 interacting genes having an important role. In contrast, inflammatory and anti-apoptotic phenotypes were predominant in CH-C. These differences would evoke different oncogenic factors in CH-B and CH-C. In conclusion, we describe the different signaling pathways induced in the livers of patients with CH-B or CH-C. The results might be useful in guiding therapeutic strategies to prevent the development of hepatocellular carcinoma in cases of CH-B and CH-C.

Adolescent↗

Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome.

Three tandem repeats of a 13-mer in the AT-rich region are essential to the unique replication origin of E. coli and of remotely related Enterobacteriaceae. These iterated sequences are identified by deletion analysis and sensitivities to endonucleases as the site for initial duplex opening by the initiator dnaA protein. This "open complex" requires ATP and 38 degrees C for optimum formation and stability. The subsequent dnaC-dependent entry of dnaB helicase to form a "prepriming complex" stabilizes the open structure, blocks cleavages by a restriction endonuclease in the 13-mer region, and broadens the endonuclease cutting pattern. We propose that dnaA protein recognizes and successively opens the 13-mer sequences, thereby guiding the entry of dnaB helicase into the duplex preparatory to priming of replication.

Adenine Nucleotides↗

Expression profiles of miRNAs in ruminant intermediate hosts with cystic echinococcosis.

Cystic echinococcosis (CE), caused by the larval stage of Echinococcus granulosus sensu lato (s.l.), is a parasitic zoonotic disease recognized by the World Health Organization as a neglected tropical disease of significant public health concern. Despite ongoing control programs, CE remains endemic, underlining the need for integrated control strategies that involve new diagnostic and therapeutic tools. Recent investigations have spotlighted microRNAs (miRNAs) as key regulators in parasite development, immunomodulation, and as potential diagnostic and therapeutic targets. In the present research, a molecular study was conducted to investigate hydatid cyst samples (protoscoleces and germinal membranes) collected in southern Italy from different ruminant species (sheep, cattle, and water buffaloes), naturally infected with CE, with the ultimate goal of establishing a more comprehensive picture of miRNA expression patterns in these intermediate hosts. The bioinformatic analysis of hydatid cyst samples revealed 168 mature miRNAs. Among these, egr-miR-10-5p, egr-let-7-5p, and egr-miR-71-5p were the most abundant, with egr-miR-10-5p showing particularly high expression levels. No significant differences in miRNA abundance between host species were found. In contrast, when focusing on the comparison between protoscoleces and sterile germinal membranes, 24 miRNAs were found to be differentially expressed. Targeted qPCR of four selected miRNAs (egr-miR-71-5p, egr-let-7-5p, egr-miR-125-5p, and egr-miR-10-5p) showed clear overexpression in protoscoleces and in fertile germinal membranes compared with sterile ones. The differential miRNA expression patterns provide insight into the molecular mechanisms controlling the parasite's lifecycle and may guide the development of novel intervention methods to enhance CE control in endemic areas.

Animals↗

Serial minimal residual disease (MRD) analysis as a predictor of response duration in Philadelphia-positive acute lymphoblastic leukemia (Ph+ALL) during imatinib treatment.

Patients with refractory or relapsed Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ALL) rarely have prolonged responses to salvage therapy, including imatinib, resulting in a short opportunity for potentially curative stem cell transplantation. To identify minimal residual disease (MRD) parameters predictive of imminent relapse, we quantitated Bcr-Abl expression by real-time PCR in peripheral blood (PB) and bone marrow (BM) of 24 Ph+ALL patients after achieving a complete response and MRD minimum. The ratio of Bcr-Abl and glyceraldehyde-3-phosphate dehydrogenase copies, magnitude of increase and velocity of increase were evaluated regarding subsequent time intervals to relapse, death or censoring. High Bcr-Abl levels >/=5 x 10(-4) in PB (n=23) and >/=10(-4) in BM (n=18) were significantly associated with short time periods to relapse. Bcr-Abl increases >2 logarithmic units (log) in PB, but not in BM preceded short-term relapse. The velocity of Bcr-Abl increases predicted response duration in PB (cutoff: 1.25 log/30 days) and BM (0.6). Bcr-Abl level and velocity of increase in BM as well as magnitude of increase in PB correlated with remaining periods of survival and predicted relapse within 2 months in nine of 10, 10 of 11 and four of four patients, respectively. Thus, these MRD parameters may guide timing and intensity of therapeutic modifications.

Antineoplastic Agents↗