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  • Analytical Chemistry and Spectroscopy  (3)
  • EXPRESSION  (2)
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  • 1
    Keywords: CELLS ; EXPRESSION ; proliferation ; SURVIVAL ; tumor ; BLOOD ; CELL ; Germany ; IN-VIVO ; KINASE ; THERAPY ; VIVO ; FOLLOW-UP ; SITE ; SITES ; GENE ; GENE-EXPRESSION ; GENES ; PROTEIN ; PROTEINS ; transcription ; METABOLISM ; TRANSDUCTION ; gene transfer ; GENE-TRANSFER ; PATIENT ; DONOR ; TRANSPLANTATION ; CONTRAST ; SUFFICIENT ; treatment ; FREQUENCY ; FREQUENCIES ; TARGET ; CELL-SURVIVAL ; PATTERNS ; gene expression ; VECTOR ; LYMPHOCYTES ; HUMAN GENOME ; REGION ; REGIONS ; PROGENITOR CELLS ; IMMUNITY ; T-LYMPHOCYTES ; T lymphocyte ; CHILDREN ; PERIPHERAL-BLOOD ; T lymphocytes ; INTEGRATION ; PATTERN ; SEVERE COMBINED IMMUNODEFICIENCY ; LEVEL ; LONG ; progenitor ; EVENTS ; USA ; in vivo ; progenitor cell ; TRANSDUCED CELLS ; RECONSTITUTION ; RETROVIRAL GENE MARKING ; RETROVIRAL INTEGRATION ; MEDICINE ; VECTOR INTEGRATION ; PROGENITOR-CELL ; SCID-X1 ; ADA
    Abstract: We treated 10 children with X-linked SCID (SCID-X1) using gammaretrovirus-mediated gene transfer. Those with sufficient follow-up were found to have recovered substantial immunity in the absence of any serious adverse events up to 5 years after treatment. To determine the influence of vector integration on lymphoid reconstitution, we compared retroviral integration sites (RISs) from peripheral blood CD3(+) T lymphocytes of 5 patients taken between 9 and 30 months after transplantation with transduced CD34(+) progenitor cells derived from 1 further patient and I healthy donor. Integration occurred preferentially in gene regions on either side of transcription start sites, was clustered, and correlated with the expression level in CD34(+) progenitors during transduction. In contrast to those in CD34(+) cells, RISs recovered from engrafted CD3(+)T cells were significantly overrepresented within or near genes encoding proteins with kinase or transferase activity or involved in phosphorus metabolism. Although gross patterns of gene expression were unchanged in transduced cells, the divergence of RIS target frequency between transduced progenitor cells and post-thymic T lymphocytes indicates that vector integration influences cell survival, engraftment, or proliferation
    Type of Publication: Journal article published
    PubMed ID: 17671654
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  • 2
    Keywords: EXPRESSION ; GENE ; DIFFERENTIATION ; IDENTIFICATION ; EMBRYONIC STEM-CELLS ; HYPERMETHYLATION ; SUPPRESSOR ; methylome ; CANCER GENOME ; CPG ISLAND SHORES
    Abstract: Epigenetic alterations, that is, disruption of DNA methylation and chromatin architecture, are now acknowledged as a universal feature of tumorigenesis. Medulloblastoma, a clinically challenging, malignant childhood brain tumour, is no exception. Despite much progress from recent genomics studies, with recurrent changes identified in each of the four distinct tumour subgroups (WNT-pathway-activated, SHH-pathway-activated, and the less-well-characterized Group 3 and Group 4), many cases still lack an obvious genetic driver. Here we present whole-genome bisulphite-sequencing data from thirty-four human and five murine tumours plus eight human and three murine normal controls, augmented with matched whole-genome, RNA and chromatin immunoprecipitation sequencing data. This comprehensive data set allowed us to decipher several features underlying the interplay between the genome, epigenome and transcriptome, and its effects on medulloblastoma pathophysiology. Most notable were highly prevalent regions of hypomethylation correlating with increased gene expression, extending tens of kilobases downstream of transcription start sites. Focal regions of low methylation linked to transcription-factor-binding sites shed light on differential transcriptional networks between subgroups, whereas increased methylation due to re-normalization of repressed chromatin in DNA methylation valleys was positively correlated with gene expression. Large, partially methylated domains affecting up to one-third of the genome showed increased mutation rates and gene silencing in a subgroup-specific fashion. Epigenetic alterations also affected novel medulloblastoma candidate genes (for example, LIN28B), resulting in alternative promoter usage and/or differential messenger RNA/microRNA expression. Analysis of mouse medulloblastoma and precursor-cell methylation demonstrated a somatic origin for many alterations. Our data provide insights into the epigenetic regulation of transcription and genome organization in medulloblastoma pathogenesis, which are probably also of importance in a wider developmental and disease context.
    Type of Publication: Journal article published
    PubMed ID: 24847876
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  • 3
    ISSN: 0935-6304
    Keywords: Gas chromatography-mass spectrometry ; Capillary columns ; Stationary phases ; Silicones ; Thermal degradation ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The applicability of capillary columns for gas chromatography is often limited by stationary phase degradation at elevated temperatures. In order to achieve a better understanding of column thermostability, column bleed products have been analyzed qualitatively by gas chromatography-mass spectrometry (GC-MS). Three silicone stationary phases were studied: SE-52, SE-54, and OV-1701. Each of these was immobilized in the columns. The proportion of cyclics containing diphenyl in column bleed from SE-52 reflected to a large extent the composition of the polymer, while for SE-54 the proportion of such cyclics was unexpectedly high. The polar moiety of OV-1701, the cyanopropyl(phenyl)siloxy unit, was found to exert a highly destabilizing effect on the polymer, and the thermal degradation products consisted mainly of cyclosiloxanes containing this unit.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0935-6304
    Keywords: Open tubular gas chromatography ; Dynamic headspace analysis ; Purge and trap ; Thermal desorption ; Reinjection ; Fourier transform infrared spectroscopy ; Volatile constituents in polymers ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An analytical system for the analysis of volatiles entrained in polymers is described. This system is based on a thermal desorption oven connected to a cold trap. After enrichment of headspace vapor, trapped material is reinjected and analyzed by open tubular gas chromatography/Fourier transform infrared spectroscopy, OTGC/FTIR. The thermal desorption oven is designed to provide different modes of sample introduction: use of a pyroprobe; insertion of a piece of quartz tubing with applied sample; or syringe injection. Headspace enrichment is carried out in a piece of fused silica capillary tubing filled with glass beads. The trap may be cooled either electrically using Peltier elements or with liquid nitrogen. A six-port rotary valve is used for flow switching between enrichment and reinjection modes. All system parameters, temperatures, and timed events, are controlled from the gas chromatograph. Dynamic headspace analysis is demonstrated as a method for polymer characterization.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 0935-6304
    Keywords: Gas chromatography, GC ; Glass and fused silica capillary columns ; Coating time and efficiency ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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