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At least 1,369 records · Page 76Linked to original sources
PubMed2006

Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development.

DNA methylation and histone methylation are two key epigenetic modifications that help govern heterochromatin dynamics. The roles for these chromatin-modifying activities in directing tissue-specific development remain largely unknown. To address this issue, we examined the roles of DNA methyltransferase 1 (Dnmt1) and the H3K9 histone methyltransferase Suv39h1 in zebra fish development. Knockdown of Dnmt1 in zebra fish embryos caused defects in terminal differentiation of the intestine, exocrine pancreas, and retina. Interestingly, not all tissues required Dnmt1, as differentiation of the liver and endocrine pancreas appeared normal. Proper differentiation depended on Dnmt1 catalytic activity, as Dnmt1 morphants could be rescued by active zebra fish or human DNMT1 but not by catalytically inactive derivatives. Dnmt1 morphants exhibited dramatic reductions of both genomic cytosine methylation and genome-wide H3K9 trimethyl levels, leading us to investigate the overlap of in vivo functions of Dnmt1 and Suv39h1. Embryos lacking Suv39h1 had organ-specific terminal differentiation defects that produced largely phenocopies of Dnmt1 morphants but retained wild-type levels of DNA methylation. Remarkably, suv39h1 overexpression rescued markers of terminal differentiation in Dnmt1 morphants. Our results suggest that Dnmt1 activity helps direct histone methylation by Suv39h1 and that, together, Dnmt1 and Suv39h1 help guide the terminal differentiation of particular tissues.

Animals↗
PubMedDate not supplied

An interventional magnetic resonance imaging technique for the molecular characterization of intraprostatic dynamic contrast enhancement.

The biological characterization of an individual patient's tumor by noninvasive imaging will have an important role in cancer care and clinical research if the molecular processes that underlie the image data are known. Spatial heterogeneity in the dynamics of magnetic resonance imaging contrast enhancement (DCE-MRI) is hypothesized to reflect variations in tumor angiogenesis. Here we demonstrate the feasibility of precisely colocalizing DCE-MRI data with the genomic and proteomic profiles of underlying biopsy tissue using a novel MRI-guided biopsy technique in a patients with prostate cancer.

Biopsy↗
PubMed2026

Multiomic study of cutaneous T-cell lymphoma reveals single-cell clonal evolution in progression and therapy resistance.

Cutaneous T-cell lymphoma (CTCL) remains a challenging disease due to its significant heterogeneity, therapy resistance, and relentless progression. Multiomics technologies offer the potential to provide uniquely precise views of disease progression and response to therapy. Here, we present a comprehensive multiomics view of CTCL clonal evolution, incorporating exome, whole-genome, epigenome, bulk, single-cell T-cell receptor, and single-cell RNA sequencing of 99 clinically annotated serial skin, peripheral blood, and lymph node samples from 34 patients with CTCL. We leveraged this extensive data set to define the molecular underpinnings of CTCL progression in individual patients at single-cell resolution with the goal of identifying clinically useful biomarkers and therapeutic targets. Our studies identified recurrent progression-associated clonal genomic alterations; we highlight mutation of CCR4, phosphoinositide 3-kinase inhibitor signaling, and programmed cell death protein 1 (PD-1) checkpoint pathways as evasion tactics deployed by malignant T cells. We identified a gain-of-function mutation in STAT3 (D661Y) and demonstrated, using cleavage under targets and release using nuclease (CUT&RUN) and RNA sequencing, that it enhances binding to and transcription of genes in Rho GTPase pathways. With our previous work implicating this pathway in histone deacetylase inhibitor-resistant CTCL, these data provide further support for a previously unrecognized role for Rho GTPase pathway dysregulation in CTCL progression. Recurrent progression-associated mutations were common in the epigenetic modifier EZH2, suggesting that EZH2 inhibition may benefit patients with CTCL. Our findings support an approach in which genomic analysis is widely used for improved disease monitoring, biomarker-informed clinical trial design, and genome-guided therapeutic decision-making. Moreover, these molecular changes present new opportunities for therapeutic targeting in this challenging and incurable cancer.

Multiomics↗
PubMed2002

Mutational analysis of the replication signals in the 3'-nontranslated region of citrus tristeza virus.

Citrus tristeza virus (CTV), a member of the Closteroviridae, has a 19.3-kb messenger-sense RNA genome consisting of 12 open reading frames with nontranslated regions (NTR) at the 5' and 3' termini. The 273 nucleotide (nt) 3'-NTR is highly conserved ( approximately 95%) among the sequenced CTV isolates in contrast to the highly diverse 5'-NTR sequences. The 3' replication signals were mapped to the 3' 234 nts within the NTR. This region of CTV does not contain a poly-A tract nor does it appear to fold as a tRNA-mimic. Instead, a computer-predicted thermodynamically stable secondary structure comprised of 10 stem-and-loop (SL) structures, referred to as SL1 to SL10 (5' to 3'), was common to all CTV isolates. This putative structure was used as a guide to examine the 3' requirements for replication in vivo. The resulting data suggest that a complex 3' structure is required for those functions that provide for efficient replication of CTV in vivo such as minus-strand initiation, regulation of strand asymmetry, effective translation of the myriad of viral mRNAs, or stability of RNAs. Deletions into the 3'-NTR, up to 66 nts from the 5' direction and 11 nts from the 3' direction, deleting or disrupting putative SL1, SL2 and SL3, or SL10, resulted in continued replication, suggesting that these sequences are not essential for basal-level replication, but are required for efficient replication. Predicted stem loops 3 through 10 were examined by mutations designed to alter the primary structures while preserving the secondary structures. Mutations designed to disrupt the predicted stems of SL3, SL5, SL7, SL9, or SL10 resulted in substantially reduced levels of replication, while compensatory mutations resulted in partial restorations of replication, suggesting that these predicted secondary structures are involved in replication. Also, the putative loop sequences of SL5, SL6, SL7, and SL9 tolerated mutagenesis with continued but reduced levels of replication. In contrast, all mutations introduced into putative SL4, SL8, and the stem of SL6 prevented replication, suggesting that the primary structure of these regions make up the core of the 3' replication signal. The 3' triplet, CCA, was shown to be necessary for efficient replication, but deletion of eleven nts to expose an internal CCA resulted in continued replication.

3' Untranslated Regions↗
PubMed2005

Disruption of cerebellar granule cell development in the Pax6 mutant, Sey mouse.

The transcriptional regulator Pax6 is expressed in cerebellar granule cells and a mutation in that gene (Sey) has been shown to affect cerebellar development. We have defined novel phenotypes in the Sey/Sey cerebellum, indicating that the mutation of Pax6 alters granule cell behavior in vitro and also the interaction between granule cells and Purkinje cells in vivo. In culture, Sey/Sey granule cell precursors show the following abnormal phenotypes: enhanced proliferation, increased apoptotic cell death, and decreased number of morphologically differentiating beta-III tubulin-positive cells. There is an overlap in the populations of Sey/Sey cells that express markers for proliferation and neuronal differentiation indicating an abnormality in the transition between these states in granule cells. In vivo, Purkinje cell ectopias were found deep in the cerebellum and extending into the inferior colliculus. Coincident with this, Purkinje cell phenotype was the alteration in the pattern and levels of Reelin expression in granule cells of the external germinal layer (EGL). The finding of increased staining for Disabled-1, a signaling pathway intermediary that is normally downregulated by a Reelin signal, throughout the Purkinje cell population suggests that in the Sey/Sey cerebellum there is a disruption in Reelin signaling from the EGL to Purkinje cells. These findings suggest that Pax6 is critical for the proper differentiation of granule cells and their communication with developing Purkinje cells. Thus, through its guidance of granule cell development, Pax6 also has a strong influence on many of the cellular programs that guide the morphogenesis of the entire cerebellum.

Animals↗
PubMed1994

Serum alanine aminotransferase measurement as a guide to selective testing for hepatitis C during medical checkup.

The efficiency of elevated serum alanine aminotransferase values for selecting subjects to be tested for hepatitis B or C infections in a large French population undergoing a medical checkup was investigated. For 5 consecutive weeks, serum alanine aminotransferase values were controlled in 9044 subjects; 308 subjects (202 males) were selected with alanine aminotransferase levels 1.2-fold above the normal value (58 iu/l for men, 34 iu/l for women). For each selected case, an age- and sex-cross-matched control was included. Of the 308 subjects with elevated alanine aminotransferase values, one was HBsAg positive and 15 (seven males) were anti-HCV positive. All anti-HCV sera tested by enzyme immunoassay were also positive by three immunoblots and 11/15 (73%) were HCV-RNA positive by reverse transcription-polymerase chain reaction. Of the 308 control subjects, two were HBsAg positive and four (two males) were weakly anti-HCV positive by enzyme immunoassay. Only one weakly anti-HCV positive serum was reactive by one immunoblot and all were HCV-RNA negative. This study shows the usefulness of alanine aminotransferase screening to detect hepatitis C virus infection in the general French population. Many of the anti-HCV positive subjects detected in this study were not aware of their hepatitis C virus seropositivity (12/15) or that they were viremic (11/15). Use of this low-cost assay will considerably reduce the number of subjects to be tested for hepatitis C virus serological status and therefore the cost. It may make possible the investigation of large populations by setting up public health programs to detect and treat hepatitis C virus. Hepatitis C virus infected subjects detected in these programs could benefit from medical follow up, including antiviral therapy.

Adolescent↗
PubMed1998

Mutations in a polycistronic nuclear gene associated with molybdenum cofactor deficiency.

All molybdoenzymes other than nitrogenase require molybdopterin as a metal-binding cofactor. Several genes necessary for the synthesis of the molybdenum cofactor (MoCo) have been characterized in bacteria and plants. The proteins encoded by the Escherichia coli genes moaA and moaC catalyse the first steps in MoCo synthesis. The human homologues of these genes are therefore candidate genes for molybdenum cofactor deficiency, a rare and fatal disease. Using oligonucleotides complementary to a conserved region in the moaA gene, we have isolated a human cDNA derived from liver mRNA. This transcript contains an open reading frame (ORF) encoding the human moaA homologue and a second ORF encoding a human moaC homologue. Mutations can be found in the majority of MoCo-deficient patients that confirm the functional role of both ORFs in the corresponding gene MOCS1 (for 'molybdenum cofactor synthesis-step 1'). Northern-blot analysis detected only full-length transcripts containing both consecutive ORFs in various human tissues. The mRNA structure suggests a translation reinitiation mechanism for the second ORF. These data indicate the existence of a eukaryotic mRNA, which as a single and uniform transcript guides the synthesis of two different enzymatic polypeptides with disease-causing potential.

Amino Acid Sequence↗
PubMed1995

Metabolic operons in Lactococci.

The genes for the biosynthesis of histidine, tryptophan and branched-chain amino acids (ilv for isoleucine, leucine and valine) are clustered in large operons. In addition to genes encoding the pathway enzymes, the his and the ilv operons contain 4 and 3 other genes, respectively. The functions of two of these, orf3 and aldB are regulatory. The second gene of the his operon, orf3, encodes a protein homologous to the histidyl-tRNA synthetases. It is involved in transcription attenuation upstream of the his operon. This regulation is related to a new class of attenuation mechanisms controlling the expression of most tRNA synthetase genes and a few metabolic operons in Gram-positive bacteria. Gene aldB, the penultimate gene of the ilv operon, encodes acetolactate decarboxylase. This enzyme transforms acetolactate (AL), the first intermediate of leucine and valine biosynthesis, into acetoin. AL decarboxylase is positively controlled by the availability of leucine and possibly valine in the cell. This is the key enzyme for a new class of regulatory mechanisms, a metabolic shunt which guides the AL flux towards synthesis of amino acids or a secondary metabolite.

Amino Acid Sequence↗
PubMed2005

A novel designed single domain antibody on 3-D structure of ricin A chain remarkably blocked ricin-induced cytotoxicity.

Ricin A chain (RA), an N-glycosidase, is able to fatally disrupt protein synthesis by attacking the Achilles heel of the ribosome RNA (rRNA). As specific immunotoxins, emergence of inhibitors for RA may obtain access to antagonistics against ricin intoxication and contribute to ameliorate the concomitant side effects. Many experimental results showed that the engineered VHs, which possessed solubility, stability, small size and consequently easier to express, purify and manipulate in vitro, were self and long-lived molecules compared to synthetic peptides. In this study, based on the crystal structure of RA, a novel recombinant human single-domain antibody expressing a polypeptide against RA in the CDR3 loop (named rVH(PT)) was obtained using computer-guided molecular design method. Theoretically, rVH(PT) could penetrate deeply into the active cleft of RA and act as a potent antagonist analogue to block the RA-rRNA interaction. Followed results showed that the recombinant VH(PT) was easily expressed of high-yield production and in a partially soluble fusion form in Escherichia coli. In vitro cytotoxicity experiments demonstrated that it possessed remarkable ability to block ricin-induced cytotoxicity. This study highlights the potential of human VH to display biostructure and biofunction of peptides designed on RA functional domain and could be useful in developing new antidotes with potential therapeutic uses to neutralize unintended exposure to ricin.

Antibodies↗
PubMed1998

Detection and clearance of prostate cells subsequent to ultrasound-guided needle biopsy as determined by multiplex nested reverse transcription polymerase chain reaction assay.

OBJECTIVES: To determine if circulating prostate cells are detectable subsequent to transrectal ultrasound (TRUS)-guided biopsy, and if so, whether cells remain in circulation for up to 4 weeks. METHODS: Blood samples were drawn from 90 patients with elevated serum prostate-specific antigen (PSA) levels and/or abnormal digital rectal examination. Two samples were drawn from all patients immediately prior to TRUS and 30 minutes postbiopsy. Blood samples were also obtained 1 week postbiopsy from 83 patients, and 1 month postbiopsy from 61 patients. Multiplex nested reverse transcription polymerase chain reaction assay (RT-PCR) for PSA and prostate-specific membrane antigen (PSM) was performed on total ribonucleic acid (RNA) from each sample. Results were reported as positive if at least one of the targets was detected. RESULTS: Of 45 patients with biopsy-proven adenocarcinoma, 22 were RT-PCR positive prebiopsy and all remained positive 30 minutes postbiopsy. Of 23 patients with adenocarcinoma who were RT-PCR negative prebiopsy, 5 (22%) converted to positive 30 minutes postbiopsy (P < 0.001). Four of these 5 patients returned to negative after 1 week or 1 month. Of 45 patients without cancer at biopsy, 32 were RT-PCR negative prebiopsy and 6 (19%) converted to positive 30 minutes postbiopsy (P < 0.001). Although four of six available samples were still positive at 1 week, all four samples available 1 month postbiopsy were negative. CONCLUSIONS: Detection of circulating prostate cells subsequent to biopsy occurred in 11 of 55 (20%) previously RT-PCR negative patients, a proportion twice that reported in the literature. We attribute this higher proportion to the simultaneous detection of PSA and PSM mRNA in our multiplex assay. Conversion rates were similar in patients regardless of biopsy result. Testing of serial postbiopsy blood demonstrates clearing of these cells by 4 weeks in most patients.

Aged↗
PubMed2002

Galectin-3 is not an universal marker of malignancy in thyroid nodular disease in children and adolescents.

Current methods of research into thyroid nodular disease (TND) based on the polymerase chain reaction (PCR) and reverse-transcription (RT) permit the detection of some markers, even in poorly cellular biological material. The findings from fine-needle aspiration biopsy (FNAB), the most commonly used procedure in TND, do not always correlate with the postoperative histopathological diagnosis, sometimes giving a false negative result. The aim of this present study was to improve the classical cytological evaluation of the material obtained with ultrasound-guided biopsy with a RT-PCR based technique in order to detect carcinoma even in a minimally invasive form. Aspirate from the 30 patients included in the study was smeared for conventional cytology (H+E and MGG staining) and the leftover material in the needle was frozen for subsequent PCR analysis. Fine-needle aspiration specimens were evaluated for the presence of galectin-3 (GAL-3), the most promising molecular marker of malignancy. As a positive control for cells of follicular origin, thyroglobulin (Tg) gene expression was performed. RT-PCR was performed on extracted RNA and with specific primers for the screened genes, based on a one-step reaction with a Biometra PCR machine. Tg expression was observed in 23 aspirates, among which 10 were positive for the expression of GAL-3 [3 cases of PTC, 1 an oxyphilic variant of FTC, 1 an oxyphilic variant of follicular adenoma (FA), 1 a foetal variant of FA, 2 of Hashimoto thyroiditis (HT) and 2 of HT with coexisting FA]. Our results are the first evidence that GAL-3 expression, previously documented in thyroid carcinoma of follicular origin, is also present in Hashimoto thyroiditis. This study reveals some limitations in nodule or multiple nodules of benign character. If the diagnosis of HT is excluded, then the usefulness of the method in the diagnosis of malignancy may still be very high.

Adolescent↗
PubMed2005

MAASE: an alternative splicing database designed for supporting splicing microarray applications.

Alternative splicing is a prominent feature of higher eukaryotes. Understanding of the function of mRNA isoforms and the regulation of alternative splicing is a major challenge in the post-genomic era. The development of mRNA isoform sensitive microarrays, which requires precise splice-junction sequence information, is a promising approach. Despite the availability of a large number of mRNAs and ESTs in various databases and the efforts made to align transcript sequences to genomic sequences, existing alternative splicing databases do not offer adequate information in an appropriate format to aid in splicing array design. Here we describe our effort in constructing the Manually Annotated Alternatively Spliced Events (MAASE) database system, which is specifically designed to support splicing microarray applications. MAASE comprises two components: (1) a manual/computational annotation tool for the efficient extraction of critical sequence and functional information for alternative splicing events and (2) a user-friendly database of annotated events that allows convenient export of information to aid in microarray design and data analysis. We provide a detailed introduction and a step-by-step user guide to the MAASE database system to facilitate future large-scale annotation efforts, integration with other alternative splicing databases, and splicing array fabrication.

Alternative Splicing↗
PubMed2005

Disruption of shape-complementarity markers to create cytotoxic variants of ribonuclease A.

Onconase (ONC), an amphibian member of the bovine pancreatic ribonuclease A (RNase A) superfamily, is in phase III clinical trials as a treatment for malignant mesothelioma. RNase A is a far more efficient catalyst of RNA cleavage than ONC but is not cytotoxic. The innate ability of ONC to evade the cytosolic ribonuclease inhibitor protein (RI) is likely to be a primary reason for its cytotoxicity. In contrast, the non-covalent interaction between RNase A and RI is one of the strongest known, with the RI.RNase A complex having a K(d) value in the femtomolar range. Here, we report on the use of the fast atomic density evaluation (FADE) algorithm to identify regions in the molecular interface of the RI.RNase A complex that exhibit a high degree of geometric complementarity. Guided by these "knobs" and "holes", we designed variants of RNase A that evade RI. The D38R/R39D/N67R/G88R substitution increased the K(d) value of the pRI.RNase A complex by 20 x 10(6)-fold (to 1.4 microM) with little change to catalytic activity or conformational stability. This and two related variants of RNase A were more toxic to human cancer cells than was ONC. Notably, these cytotoxic variants exerted their toxic activity on cancer cells selectively, and more selectively than did ONC. Substitutions that further diminish affinity for RI (which has a cytosolic concentration of 4 microM) are unlikely to produce a substantial increase in cytotoxic activity. These results demonstrate the utility of the FADE algorithm in the examination of protein-protein interfaces and represent a landmark towards the goal of developing chemotherapeutics based on mammalian ribonucleases.

Algorithms↗
PubMed2006

High-resolution computational models of genome binding events.

Direct physical information that describes where transcription factors, nucleosomes, modified histones, RNA polymerase II and other key proteins interact with the genome provides an invaluable mechanistic foundation for understanding complex programs of gene regulation. We present a method, joint binding deconvolution (JBD), which uses additional easily obtainable experimental data about chromatin immunoprecipitation (ChIP) to improve the spatial resolution of the transcription factor binding locations inferred from ChIP followed by DNA microarray hybridization (ChIP-Chip) data. Based on this probabilistic model of binding data, we further pursue improved spatial resolution by using sequence information. We produce positional priors that link ChIP-Chip data to sequence data by guiding motif discovery to inferred protein-DNA binding sites. We present results on the yeast transcription factors Gcn4 and Mig2 to demonstrate JBD's spatial resolution capabilities and show that positional priors allow computational discovery of the Mig2 motif when a standard approach fails.

Base Sequence↗
PubMed2003

RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs.

By generating a specialised cDNA library from four different developmental stages of Drosophila melanogaster, we have identified 66 candidates for small non-messenger RNAs (snmRNAs) and have confirmed their expression by northern blot analysis. Thirteen of them were expressed at certain stages of D.melanogaster development, only. Thirty-five species belong to the class of small nucleolar RNAs (snoRNAs), divided into 15 members from the C/D subclass and 20 members from the H/ACA subclass, which mostly guide 2'-O-methylation and pseudouridylation, respectively, of rRNA and snRNAs. These also include two outstanding C/D snoRNAs, U3 and U14, both functioning as pre-rRNA chaperones. Surprisingly, the sequence of the Drosophila U14 snoRNA reflects a major change of function of this snoRNA in Diptera relative to yeast and vertebrates. Among the 22 snmRNAs lacking known sequence and structure motifs, five were located in intergenic regions, two in introns, five in untranslated regions of mRNAs, eight were derived from open reading frames, and two were transcribed opposite to an intron. Interestingly, detection of two RNA species from this group implies that certain snmRNA species are processed from alternatively spliced pre-mRNAs. Surprisingly, a few snmRNA sequences could not be found on the published D.melanogaster genome, which might suggest that more snmRNA genes (as well as mRNAs) are hidden in unsequenced regions of the genome.

Animals↗
PubMed2007

Comparison of fresh and predegenerated muscle-vein-combined guides for the repair of rat median nerve.

Over the last 10 years, we have investigated a particular type of bioengineered nerve guide, the muscle-vein-combined tube, which is made by filling a vein with skeletal muscle. In our previous studies we have always used fresh skeletal muscle to fill vein conduits. In the present study we compared the use of fresh and predegenerated (freeze-thawed) skeletal muscle for muscle-vein-combined nerve guides. In this study, a 10-mm-long rat median nerve defect was repaired using either type of nerve guide. The samples were analyzed 5 and 30 days after surgery by light and electron microscopy. In addition, reverse transcription polymerase chain reaction (RT-PCR) was carried out to investigate the expression of mRNAs coding for glial markers, as well as glial growth factor (NRG1) and its receptors (erbB2 and erbB3). Results showed differences between the two types of nerve guides at postoperative day 5; however, no difference was detected at day 30 suggesting that both types of tissue-engineered conduit are effective for repairing peripheral nerve defects in this experimental model.

Animals↗
PubMed2006

Estrogen receptor-beta regulates psoriasin (S100A7) in human breast cancer.

We have previously observed a paradoxical relationship of the psoriasin/S100A7 gene with estrogen response in-vitro in ERalpha positive cells but its association with ERalpha negative status in-vivo raising the possibility that S100A7 might be regulated by ERbeta in breast cancer. Using doxycycline-inducible ERbeta and ERalpha expressing MCF-7 cells the hypothesis that psoriasin/S100A7 is ERbeta regulated was investigated To explore the relationship between psoriasin/S100A7 and ERbeta expression in-vivo, we also assessed a cohort of 233 ERalpha negative breast tumors using tissue microarrays and immunohistochemistry. Psoriasin/S100A7 was increased by 17beta-estradiol (E2) following ERbeta induction, in several clones of ERbeta over-expressing but not in the original MCF-7 cells, nor clones over-expressing ERalpha. The effect of E2 on psoriasin/S100A7 was inhibited by 4-hydroxytamoxifen and ICI 182780 but not with a selective ERalpha antagonist. An ERbeta selective-agonist but not an ERalpha selective-agonist, induced psoriasin/S100A7. This induction still occurred after stable down-regulation of ERalpha using siRNA in ERbeta inducible cells. E2 increased psoriasin/S100A7 mRNA but cycloheximide treatment inhibited this effect. A relationship between ERbeta and psoriasin/S100A7 was observed in the p53 immunohistochemically negative subset of invasive breast tumors in-vivo (r = 0.225, p = 0.046, n = 79). In conclusion we demonstrate that E2 induction of psoriasin/S100A7 can be specifically regulated through ERbeta in-vitro and associated with ERbeta in-vivo. These data support the hypothesis that psoriasin/S100A7 is specifically regulated by ERbeta activity and could be useful to guide future therapies targeting ERbeta in certain phenotypic subsets of breast cancers in-vivo.

Breast Neoplasms↗