Transcriptional functions of DNA Topoisomerases at a genome-wide scale and a single gene levels

The DNA topology is an important modifier of DNA functions. Torsional stress is generated when right handed DNA is either over- or underwound, producing structural deformations which drive or are driven by processes such as replication, transcription, recombination and repair. DNA topoisomerases are molecular machines that regulate the topological state of the DNA in the cell. These enzymes accomplish this task by either passing one strand of the DNA through a break in the opposing strand or by passing a region of the duplex from the same or a different molecule through a double-stranded cut generated in the DNA. Because of their ability to cut one or two strands of DNA they are also target for some of the most successful anticancer drugs used in standard combination therapies of human cancers. An effective anticancer drug is Camptothecin (CPT) that specifically targets DNA topoisomerase 1 (TOP 1). The research project of the present thesis has been focused on the role of human TOP 1 during transcription and on the transcriptional consequences associated with TOP 1 inhibition by CPT in human cell lines. Previous findings demonstrate that TOP 1 inhibition by CPT perturbs RNA polymerase (RNAP II) density at promoters and along transcribed genes suggesting an involvement of TOP 1 in RNAP II promoter proximal pausing site. Within the transcription cycle, promoter pausing is a fundamental step the importance of which has been well established as a means of coupling elongation to RNA maturation. By measuring nascent RNA transcripts bound to chromatin, we demonstrated that TOP 1 inhibition by CPT can enhance RNAP II escape from promoter proximal pausing site of the human Hypoxia Inducible Factor 1 (HIF-1) and c-MYC genes in a dose dependent manner. This effect is dependent from Cdk7/Cdk9 activities since it can be reversed by the kinases inhibitor DRB. Since CPT affects RNAP II by promoting the hyperphosphorylation of its Rpb1 subunit the findings suggest that TOP 1inhibition by CPT may increase the activity of Cdks which in turn phosphorylate the Rpb1 subunit of RNAP II enhancing its escape from pausing. Interestingly, the transcriptional consequences of CPT induced topological stress are wider than expected. CPT increased co-transcriptional splicing of exon1 and 2 and markedly affected alternative splicing at exon 11. Surprisingly despite its well-established transcription inhibitory activity, CPT can trigger the production of a novel long RNA (5’aHIF-1) antisense to the human HIF-1 mRNA and a known antisense RNA at the 3’ end of the gene, while decreasing mRNA levels. The effects require TOP 1 and are independent from CPT induced DNA damage. Thus, when the supercoiling imbalance promoted by CPT occurs at promoter, it may trigger deregulation of the RNAP II pausing, increased chromatin accessibility and activation/derepression of antisense transcripts in a Cdks dependent manner. A changed balance of antisense transcripts and mRNAs may regulate the activity of HIF-1 and contribute to the control of tumor progression After focusing our TOP 1 investigations at a single gene level, we have extended the study to the whole genome by developing the “Topo-Seq” approach which generates a map of genome-wide distribution of sites of TOP 1 activity sites in human cells. The preliminary data revealed that TOP 1 preferentially localizes at intragenic regions and in particular at 5’ and 3’ ends of genes. Surprisingly upon TOP 1 downregulation, which impairs protein expression by 80%, TOP 1 molecules are mostly localized around 3’ ends of genes, thus suggesting that its activity is essential at these regions and can be compensate at 5’ ends. The developed procedure is a pioneer tool for the detection of TOP 1 cleavage sites across the genome and can open the way to further investigations of the enzyme roles in different nuclear processes.

Mechanistic study of the effects of 8-oxo-7,8-dihydroguanine (8-oxoG) on reporter gene expression in mammalian cells

DNA damage causes replication errors, leading to genetic instability or cell death. Besides that, many types of DNA base modifications have been shown to interfere with transcriptional elongation if they are located in the transcribed DNA strand of active genes, acting as roadblocks for RNA polymerases. It is widely assumed that transcription blockage by endogenous DNA damage is responsible for the early cell senescence in organs and accelerated ageing observed in individuals with compromised nucleotide excision repair.rnThe aims of this work were to design new experimental systems for testing transcription blocking potentials of DNA base modifications in an individual gene and to apply these test systems to the investigation of the effects of a frequent endogenously generated base modification, namely 8-oxo-7,8-hydroxyguanine (8-oxoG), on the gene transcription in cells. Several experimental strategies were employed for this purpose. First, I constructed an episomal vector encoding for a short-lived EGFP-ODC fusion protein and measured expression of the reporter gene in permanently transfected clonal cell lines exposed to DNA damaging agents. Second, the expression of plasmid-borne EGFP gene damaged with photosensitisers to obtain one or several oxidative purine modifications per plasmid molecule was determined in transiently transfected human and mouse host cells in an approach known as “host cell reactivation”. As a prerequisite for these experiments, a robust method of precise quantitative measurement of the EGFP gene expression in transiently transfected cells by flow cytometry was developed and validated. Third, I elaborated a very efficient procedure for insertion of synthetic oligonucleotides carrying 8-oxoG into plasmid DNA, avoiding any unwanted base damage and strand breaks. The consequences of 8-oxoG placed in defined positions in opposing DNA strands of the EGFP gene for transcription were measured by host cell reactivation in cells with functional 8-oxoguanine DNA glycosylase (OGG1) gene and in OGG1 null cells.rnThe results obtained in Ogg1-/- cells demonstrated that unrepaired 8-oxoG, even if situated in the transcribed DNA strand, does not have any negative effect on the reporter gene transcription. On the other hand, as few as one 8-oxoG was sufficient to cause a significant decrease of the gene expression in OGG1-proficient cell lines, i.e. in the presence of base excision repair. For two analysed positions of 8-oxoG in the plasmid DNA, the inhibition of gene transcription by the base modification correlated with the efficiency of its excision by purified OGG1 protein under cell-free conditions. Based on these findings, it has to be concluded that the observed decrease of transcription is mediated by excision of the base modification by OGG1 and probably caused by the repair-induced single-strand breaks. The mechanism of transcription inhibition by 8-oxoG is therefore clearly distinct from stalling of elongating RNA polymerase II complexes at the modified base.

Bioverkapselung lebender Bakterien (Escherichia coli) mit Poly-(Silicat) nach Transformation mit dem Silicatein-alpha-Gen

Die Bioverkapselung ist eine faszinierende Methode, um biologische Materialien einschließlich Zellen in Siliziumdioxid, Metalloxiden oder hybriden Sol-Gel-Polymeren zu immobilisieren. Bisher wurde nur die Sol-Gel-Vorläufertechnologie genutzt, um Bakterien- oder Hefezellen in Siliziumdioxid zu immobilisieren. Hierfür wurden verschiedene Reagenzien als wässrige Vorläufer getestet, um poly(Silicate) auf Biomolekülen (Bhatia et al., 2000) oder Zellen (Liu und Chen 1999; Coradin und Livage, 2007) zu bilden. Einer der erfolgreichsten bisherigen Methoden verwendet eine Mischung aus Silicaten und kolloidalem Silica. Diese initialen Vorläufer werden durch die Zugabe von Salzsäure neutralisiert, was die Gelbildung fortschreiten lässt und die Verkapselung von Bakterien in einem Silica-Netzwerk zur Folge hat (Nassif et al., 2003). Mit der Entdeckung von Silicatein, einem Enzym, das aus Demospongien isoliert wurde und die Bildung von poly(Silicat) katalysiert, wurde es möglich, poly(Silicat) unter physiologischen Bedingungen zu synthetisieren. Silicatein wurde rekombinant in E. coli hergestellt und ist in der Lage, bei Raumtemperatur, neutralem pH-Wert und in wässrigen Puffersystemen aus Siliziumalkoxiden poly(Silicat) zu bilden (Krasko et al., 2000; Müller et al., 2007b; Zhou et al., 1999). In vivo katalysiert Silicatein die Synthese der Silicathülle der Schwamm-Spiculae (Skelettelemente; Müller et al., 2005b; Müller et al., 2007a; Müller et al., 2007b; Schröder et al., 2007a). Dieses Biosilica wurde in Form von Silica-Nanospheren mit Durchmessern zwischen 100 nm und 250 nm organisiert vorgefunden (Pisera 2003; Tahir et al., 2005). Mit dieser Arbeit konnte gezeigt werden, dass Escherichia coli erfolgreich mit dem Silicatein-Gen transformiert werden kann. Das Level der Proteinexpression kann in Anwesenheit von Isopropyl-β-D-thiogalaktopyranosid (IPTG) effizient erhöht werden, indem man die Bakterienzellen gleichzeitig mit Kieselsäure inkubiert. Dieser Effekt konnte sowohl auf Ebene der Synthese des rekombinanten Proteins durch Western Blot als auch durch Immunfluoreszenzmikroskopie nachgewiesen werden. Das heterolog produzierte Silicatein besitzt enzymatische Aktivität und kann die Polymerisation von Kieselsäure katalysieren. Dies konnte sowohl durch Färbung mit Rhodamin123, als auch durch Reaktion der nicht polymerisierten, freien Kieselsäure mit dem ß-Silicomolybdato-Farbsystem (Silicomolybdänblau) nachgewiesen werden. Elektronenmikroskopische Untersuchungen zeigten, dass nur die silicateinexprimierenden Bakterien während des Wachstums in Anwesenheit von Kieselsäure eine viskose Hülle um Zelle herum bilden. Ebenfalls konnte gezeigt werden, dass Silicatein-α aus Suberites domuncula nach Transformation in E. coli an die Zelloberfläche dieser Zellen transportiert wurde und dort seine enzymatische Funktion beibehielt. Die Silicathülle wurde mittels Raster-Elektronenmikroskopie (REM) analysiert. Die Bakterien, die Silicatein exprimierten und poly(Silicat) an ihrer Oberfläche synthetisierten, zeigten die gleichen Wachstumsraten wie die Bakterien, die das Gen nicht enthielten. Schlussfolgernd lässt sich sagen, dass die silicateinvermittelte Verkapselung von Bakterien mit poly(Silicat) die Bandbreite der Anwendung von Bakterien für die Produktion von rekombinanten Proteinen verbessern, erweitern und optimieren könnte.

Synthese und Charakterisierung zylindrischer Poly(2-oxazolin)bürsten als Nanocarrier für Drug Delivery Systeme

Inspiriert durch natürlich vorkommende Peptide, sind Poly(2-oxazoline) vielversprechende Kandidaten für Anwendungen in Bereichen des kontrollierten Wirkstoff- bzw. Gentransportes, wie die moderne Biomedizin dies fordert. Da Polyoxazoline als strukturisomere Amide von natürlichen Polypeptiden aufgefasst werden können, zeigen diese synthetischen Polymere in direktem Vergleich erhebliche Vorteile etwa hinsichtlich Zytotoxizät und Effizienz, was wesentlich dazu beitragen kann, aktuelle Hürden biomedizinischer Fragestellungen hinsichtlich Transport und Targeting zu überwinden. Darüber hinaus sollten zylindrische Polymerbürsten aufgrund ihrer molekularen, architekturbedingten Formanisotropie und jüngsten Ergebnissen insbesondere zur formabhängigen Endozytose sehr aussichtsreiche Kandidaten für den Einsatz zum Wirkstofftransport sein.rnrnDie vorliegende Arbeit widmete sich deshalb der Synthese und Charakterisierung von biokompatiblen zylindrischen Poly(2-oxazolin)bürsten als potentielle Nanotransporter von Wirkstoffen, Biomolekülen oder genetischem Material. Als Monomer wurde zunächst 2-Isopropyloxazolin gewählt, da das Polymer eine Phasenübergangstemperatur von 37 °C besitzt, was für Konjugatsynthesen wie auch diverse biomedizinische Applikationen interessant sein kann. Durch terminierende Methacrylamid Funktionalisierung der lebenden kationischen Oxazolinpolymerisation bzw. nachfolgende Endgruppen Transferreaktionen sind Makromonomere im Bereich 1000-5000 g/mol zugänglich. Erstmals gelang es so 2-Oxazolin basierte, hochmolekulare zylindrische Bürsten mit Konturlängen im Bereich von 250 nm mittels „Grafting Through“ Technik in freier radikalischer Polymerisation herzustellen.rnrnAusgehend von der entwickelten Syntheseroute konnten so neben Homo- und Blockcopolymerbürsten von 2-Ethyl-2-oxazolin und 2-Isopropyl-2-oxazolin auch Bürstenmoleküle aus statistischen Copolymeren von 2-Ethyl-2-oxazolin und unsubstituiertem 2-Oxazolin hergestellt werden. Während letztere die Einführung kationischer Gruppen durch selektivere Abspaltmethoden der Formylreste erlauben und so etwa DNA/RNA Komplexierungen ermöglichen können, bietet andererseits der in dieser Arbeit erstmalig demonstrierte Einsatz Azid-funktionalisierter Initiatoren zur kationischen Oxazolinpolymerisation unter Beibehaltung aller anderen sonstigen Reaktionsschritte auch die Möglichkeit der Synthese Azid-Endgruppen-funktionalisierter Makromonomere. Die „Grafting Through“ Methodik der freien radikalischen Makromonomer Polymerisation ist selbst bei diesen funktionalisierten Systemen von großem Vorteil, erlaubt sie auch hier den Zugang zu hochmolekularen Substraten mit einem Pfropfungs- bzw. Funktionalisierungsgrad von 100 %, da jede Seitenkette dieser zylindrischen Bürsten die aussenliegende, und damit sterisch leichter zugängliche funktionale Gruppe trägt. Dabei gelang es die Syntheseroute so zu gestalten, dass es möglich war alle vorgestellten Polymerbürsten mittels statischer und dynamischer Lichtstreuung hinsichtlich absoluter Molmasse und molekularer Dimension zu charakterisieren.rnIn weitereren Reaktionen konnten dann reaktive Fluoreszenzfarbstoffe mit Hilfe kupferfreier 1,3 dipolarerer Addition (kupferfreie „Click-Chemie“) an die Azid-funktionalisierten Polymerbürsten angebunden werden, so dass eine wesentliche Voraussetzung für die Detektion in in vivo und in vitro Experimenten erfüllt werden kann. Darüber hinaus gelingt die quantitative polymeranaloge Umsetzung der Azid- zu Aminogruppen durch eine polymeranalog geführte Reduktion nach Staudinger; damit können an diesen Systemen auch etablierte Konjugationstechniken an Aminogruppen durchgeführt werden. Zudem erlauben die Aminogruppen-haltigen Polymerbürsten durch Protonierung schon bei physiologischem pH die Komplexierung von DNA oder RNA. rnrnErste Lichtstreumessungen in Blutserum zeigen im Falle der kationischen Aminogruppen tragenden Polymerbürsten zwar Aggregation, was aber durch entsprechende Umsetzung nach Konjugation wahrscheinlich unterdrückt werden kann, zeigen doch die entsprechenden Precursorpolymerbürsten mit Azidgruppen in Serum keinerlei Aggregation.rnrnZellaufnahmestudien in dendritische Zellen zeigen nur im Falle einer Azid-funktionalisierten Poly(2-isopropyl-2-oxazolin)bürste eine unspezifische Aufnahme. Die hydrophileren Poly(2-oxazolin)bürsten weise keine unspezifische Aufnahme auf, was eine wichtige Anfoderung für die Verwendung als Polymercarrier in der Krebsimmuntherapie ist.rn

Consequences of DNA damage for gene transcription : direct effects of modified nucleobases and the role of base excision repair = Folgen von DNA-Schäden für die Gentranskription

The presence of damaged nucleobases in DNA can negatively influence transcription of genes. One of the mechanisms by which DNA damage interferes with reading of genetic information is a direct blockage of the elongating RNA polymerase complexes – an effect well described for bulky adducts induced by several chemical substances and UV-irradiation. However, other mechanisms must exist as well because many of the endogenously occurring non-bulky DNA base modifications have transcription-inhibitory properties in cells, whilstrnnot constituting a roadblock for RNA polymerases under cell free conditions. The inhibition of transcription by non-blocking DNA damage was investigated in this work by employing the reporter gene-based assays. Comparison between various types of DNA damage (UV-induced pyrimidine photoproducts, oxidative purine modifications induced by photosensitisation, defined synthetic modified bases such as 8-oxoguanine and uracil, and sequence-specific single-strand breaks) showed that distinct mechanisms of inhibition of transcription can be engaged, and that DNA repair can influence transcription of the affectedrngenes in several different ways.rnQuantitative expression analyses of reporter genes damaged either by the exposure of cells to UV or delivered into cells by transient transfection supported the earlier evidence that transcription arrest at the damage sites is the major mechanism for the inhibition of transcription by this kind of DNA lesions and that recovery of transcription requires a functional nucleotide excision repair gene Csb (ERCC6) in mouse cells. In contrast, oxidisedrnpurines generated by photosensitisation do not cause transcriptional blockage by a direct mechanism, but rather lead to transcriptional repression of the damaged gene which is associated with altered histone acetylation in the promoter region. The whole chain of events leading to transcriptional silencing in response to DNA damage remains to be uncovered. Yet, the data presented here identify repair-induced single-strand breaks – which arise from excision of damaged bases by the DNA repair glycosylases or endonucleases – as arnputative initiatory factor in this process. Such an indirect mechanism was supported by requirement of the 8-oxoguanine DNA glycosylase (OGG1) for the inhibition of transcription by synthetic 8-oxodG incorporated into a reporter gene and by the delays observed for the inhibition of transcription caused by structurally unrelated base modifications (8-oxoguanine and uracil). It is thereby hypothesized that excision of the modified bases could be a generalrnmechanism for inhibition of transcription by DNA damage which is processed by the base excision repair (BER) pathway. Further gene expression analyses of plasmids containing single-strand breaks or abasic sites in the transcribed sequences revealed strong transcription inhibitory potentials of these lesions, in agreement with the presumption that BER intermediates are largely responsible for the observed effects. Experiments with synthetic base modifications positioned within the defined DNA sequences showed thatrninhibition of transcription did not require the localisation of the lesion in the transcribed DNA strand; therefore the damage sensing mechanism has to be different from the direct encounters of transcribing RNA polymerase complexes with DNA damage.rnAltogether, this work provides new evidence that processing of various DNA basernmodifications by BER can perturb transcription of damaged genes by triggering a gene silencing mechanism. As gene expression can be influenced even by a single DNA damage event, this mechanism could have relevance for the endogenous DNA damage induced in cells under normal physiological conditions, with a possible link to gene silencing in general.

Primer extension based quantitative polymerase chain reaction reveals consistent differences in the methylation status of the MGMT promoter in diffusely infiltrating gliomas (WHO grade II-IV) of adults

Diffusely infiltrating gliomas (WHO grade II-IV) are the most common primary brain tumours in adults. These tumours are not amenable to cure by surgery alone, so suitable biomarkers for adjuvant modalities are required to guide therapeutic decision-making. Epigenetic silencing of the O(6)-methylguanine-DNA methyltransferase (MGMT) gene by promoter methylation has been associated with longer survival of patients with high-grade gliomas who receive alkylating chemotherapy; and molecular testing for the methylation status of the MGMT promoter sequence is regarded as among the most relevant of such markers. We have developed a primer extension-based assay adapted to formalin-fixed paraffin-embedded tissues that enables quantitative assessment of the methylation status of the MGMT promoter. The assay is very sensitive, highly reproducible, and provides valid test results in nearly 100% of cases. Our results indicate that oligodendrogliomas, empirically known to have a relatively favourable prognosis, are also the most homogeneous entities in terms of MGMT promoter methylation. Conversely, astrocytomas, which are more prone to spontaneous progression to higher grade malignancy, are significantly more heterogeneous. In addition, we show that the degree of promoter methylation correlates with the prevalence of loss of heterozygosity on chromosome arm 1p in the oligodendroglioma group, but not the astrocytoma group. Our results may have potentially important implications for clinical molecular diagnosis.

Type 2 diabetes is associated with reduced ATP-binding cassette transporter A1 gene expression, protein and function

Objective Increasing plasma glucose levels are associated with increasing risk of vascular disease. We tested the hypothesis that there is a glycaemia-mediated impairment of reverse cholesterol transport (RCT). We studied the influence of plasma glucose on expression and function of a key mediator in RCT, the ATP binding cassette transporter-A1 (ABCA1) and expression of its regulators, liver X receptor-α (LXRα) and peroxisome proliferator-activated receptor–γ (PPARγ). Methods and Results Leukocyte ABCA1, LXRα and PPARγ expression was measured by polymerase chain reaction in 63 men with varying degrees of glucose homeostasis. ABCA1 protein concentrations were measured in leukocytes. In a sub-group of 25 men, ABCA1 function was quantified as apolipoprotein-A1-mediated cholesterol efflux from 2–3 week cultured skin fibroblasts. Leukocyte ABCA1 expression correlated negatively with circulating HbA1c and glucose (rho = −0.41, p<0.001; rho = −0.34, p = 0.006 respectively) and was reduced in Type 2 diabetes (T2DM) (p = 0.03). Leukocyte ABCA1 protein was lower in T2DM (p = 0.03) and positively associated with plasma HDL cholesterol (HDL-C) (rho = 0.34, p = 0.02). Apolipoprotein-A1-mediated cholesterol efflux correlated negatively with fasting glucose (rho = −0.50, p = 0.01) and positively with HDL-C (rho = 0.41, p = 0.02). It was reduced in T2DM compared with controls (p = 0.04). These relationships were independent of LXRα and PPARγ expression. Conclusions ABCA1 expression and protein concentrations in leukocytes, as well as function in cultured skin fibroblasts, are reduced in T2DM. ABCA1 protein concentration and function are associated with HDL-C levels. These findings indicate a glycaemia- related, persistent disruption of a key component of RCT.

Gene expression of tumour necrosis factor and insulin signalling-related factors in subcutaneous adipose tissue during the dry period and in early lactation in dairy cows

Gene expression of adipose factors, which may be part of the mechanisms that underlie insulin sensitivity, were studied in dairy cows around parturition. Subcutaneous fat biopsies and blood samples were taken from 27 dairy cows in week 8 antepartum (a.p.), on day 1 postpartum (p.p.) and in week 5 p.p. In the adipose tissue samples, mRNA was quantified by real-time reverse transcription polymerase chain reaction for tumour necrosis factor alpha (TNFalpha), insulin-independent glucose transporter (GLUT1), insulin-responsive glucose transporter (GLUT4), insulin receptor, insulin receptor substrate 1 (IRS1), insulin receptor substrate 2 (IRS2), regulatory subunit of phosphatidylinositol-3 kinase (p85) and catalytic subunit of phosphatidylinositol-3 kinase. Blood plasma was assayed for concentrations of glucose, beta-hydroxybutyric acid, non-esterified fatty acids (NEFA) and insulin. Plasma parameters followed a pattern typically observed in dairy cows. Gene expression changes were observed, but there were no changes in TNFalpha concentrations, which may indicate its local involvement in catabolic adaptation of adipose tissue. Changes in GLUT4 and GLUT1 mRNA abundance may reflect their involvement in reduced insulin sensitivity and in sparing glucose for milk synthesis in early lactation. Unchanged gene expression of IRS1, IRS2 and p85 over time may imply a lack of their involvement in terms of insulin sensitivity dynamics. Alternatively, it may indicate that post-transcriptional modifications of these factors came into play and may have concealed an involvement.

The bovine aristaless-like homeobox 4 (ALX4) as a candidate gene for syndactyly

The ALX4 (aristaless-like homeobox 4) gene encodes a paired-type homeodomain transcriptional activator and plays a major role in anterior-posterior pattern formation during limb development. Here, the cloning, genomic structure and expression of the bovine ortholog of the ALX4 gene are reported. The bovine ALX4 gene consists of four exons and is located on BTA15q28-->q29 in a region syntenic to HSA11p11.2. The transcribed ALX4 mRNA encodes a 397-amino-acid protein showing a paired-type homeodomain and a C-terminal stretch of amino acids known as the OAR- or aristaless domain. The predicted protein shares 92.5% identity to human and mouse ALX4 proteins and all three species share almost complete identity in the conserved domains. ALX4 expression was detected by reverse transcriptase polymerase chain reaction in bovine fetal limb bones. The ALX4 gene was evaluated as a candidate gene for bovine syndactyly which has been mapped on the telomeric region of cattle chromosome 15. Sequencing of the four exons with flanking sequences of the bovine ALX4 gene from a panel of 14 affected animals belonging to German Holstein, German Fleckvieh and crossbreds, and 27 unaffected individuals from German Holstein revealed five silent SNPs within the coding region out of eleven SNPs in total. Four SNPs were polymorphic in the affected animals, but in comparison to the genotyped unaffected individuals the genotype distribution showed no evidence for an association to the phenotype. Therefore our data indicate that the ALX4 gene can probably be excluded as candidate gene for bovine syndactyly in the examined animals.

Gene expression in skeletal muscle of coronary artery disease patients after concentric and eccentric endurance training

Low-intensity concentric (CET) and eccentric (EET) endurance-type training induce specific structural adaptations in skeletal muscle. We evaluated to which extent steady-state adaptations in transcript levels are involved in the compensatory alterations of muscle mitochondria and myofibrils with CET versus EET at a matched metabolic exercise intensity of medicated, stable coronary patients (CAD). Biopsies were obtained from vastus lateralis muscle before and after 8 weeks of CET (n=6) or EET (n=6). Transcript levels for factors involved in mitochondrial biogenesis (PGC-1alpha, Tfam), mitochondrial function (COX-1, COX-4), control of contractile phenotype (MyHC I, IIa, IIx) as well as mechanical stress marker (IGF-I) were quantified using an reverse-transcriptase polymerase chain reaction approach. After 8 weeks of EET, a reduction of the COX-4 mRNA level by 41% and a tendency for a drop in Tfam transcript concentration (-33%, P=0.06) was noted. This down-regulation corresponded to a drop in total mitochondrial volume density. MyHC-IIa transcript levels were specifically decreased after EET, and MyHC-I mRNA showed a trend towards a reduction (P=0.08). Total fiber cross-sectional area was not altered. After CET and EET, the IGF-I mRNA level was significantly increased. The PGC-1alpha significantly correlated with Tfam, and both PGC-1alpha and Tfam significantly correlated with COX-1 and COX-4 mRNAs. Post-hoc analysis identified significant interactions between the concurrent medication and muscular transcript levels as well as fiber size. Our findings support the concept that specific transcriptional adaptations mediate the divergent mitochondrial response of muscle cells to endurance training under different load condition and indicate a mismatch of processes related to muscle hypertrophy in medicated CAD patients.

Cyclin D1 (CCND1) A870G gene polymorphism modulates smoking-induced lung cancer risk and response to platinum-based chemotherapy in non-small cell lung cancer (NSCLC) patients

PURPOSE: The cyclin D1 (CCND1) A870G gene polymorphism is linked to the outcome in patients with resectable non-small cell lung cancer (NSCLC). Here, we investigated the impact of this polymorphism on smoking-induced cancer risk and clinical outcome in patients with NSCLC stages I-IV. METHODS: CCND1 A870G genotype was determined by polymerase chain reaction (PCR) and restriction fragment length polymorphism analysis (RFLP) of DNA extracted from blood. The study included 244 NSCLC patients and 187 healthy control subjects. RESULTS: Patient characteristics were: 70% male, 77% smokers, 43% adenocarcinoma, and 27% squamous cell carcinoma. Eighty-one percent of the patients had stages III-IV disease. Median age at diagnosis was 60 years and median survival was 13 months. Genotype frequencies of patients and controls both conformed to the Hardy Weinberg equilibrium. The GG genotype significantly correlated with a history of heavy smoking (>or=40 py, P=0.02), and patients with this genotype had a significantly higher cigarette consumption than patients with AA/AG genotypes (P=0.007). The GG genotype also significantly correlated with tumor response or stabilization after a platinum-based first-line chemotherapy (P=0.04). Survival analysis revealed no significant differences among the genotypes. CONCLUSION: Evidence was obtained that the CCND1 A870G gene polymorphism modulates smoking-induced lung cancer risk. Further studies are required to explore the underlying molecular mechanisms and to test the value of this gene polymorphism as a predictor for platinum-sensitivity in NSCLC patients.

The -308 tumour necrosis factor-alpha gene polymorphism predicts therapeutic response to TNFalpha-blockers in rheumatoid arthritis and spondyloarthritis patients

OBJECTIVE: To examine whether the G-to-A polymorphism at position -308 in the promoter of the tumour necrosis factor-alpha (TNFalpha) gene influences the therapeutic response to TNFalpha-blockers in patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA) and ankylosing spondylitis (AS). METHODS: A total of 54 patients with RA, 10 with PsA and 22 with AS were genotyped by polymerase chain reaction for the -308 TNFalpha promoter polymorphism. They were treated with infliximab (n = 63), adalimumab (n = 10) or etanercept (n = 13). Clinical response was assessed after 24 weeks by the Disease Activity Score in 28 joints (DAS28) for RA and PsA, and the Bath Ankylosing Spondylitis Activity Index (BASDAI) for AS patients. RESULTS: All patients with the A/A genotype (n = 3, all RA) and two patients with the A/G genotype (AS) failed to respond to anti-TNF treatment. Irrespective of the underlying disease, moderate response (n = 44) was predominantly associated with the A/G genotype (A/G 18/22, G/G 4/22), whereas good response (n = 59) was exclusively seen in patients with the G/G genotype. The average improvement in the DAS28 score was 0.83 in the A/A, 1.50 in the A/G and 2.64 in the G/G group of RA and PsA patients (P < 0.0001). The BASDAI score in AS improved on average by 1.21 in the A/G and by 3.30 in the G/G group (P < 0.005). CONCLUSIONS: The data suggest that humans with a TNFalpha -308 G/G genotype are better responders to anti-TNFalpha treatment than those with A/A or A/G genotypes independent of the treated rheumatic disease (RA, PsA or AS).

Gene expression by human monocytes from peripheral blood in response to exposure to metals

With increasing life expectancy and active lifestyles, the longevity of arthroplasties has become an important problem in orthopaedic surgery and will remain so until novel approaches to joint preservation have been developed. The sensitivity of the recipient to the metal alloys may be one of the factors limiting the lifespan of implants. In the present study, the response of human monocytes from peripheral blood to an exposure to metal ions was investigated, using the method of real-time polymerase chain reaction (PCR)-based low-density arrays. Upon stimulation with bivalent (Co2+ and Ni2+) and trivalent (Ti3+) cations and with the calcium antagonist LaCl3, the strength of the elicited monocytic response was in the order of Co2+ > or = Ni2+ > Ti3+ > or = LaCl3. The transcriptional regulation of the majority of genes affected by the exposure of monocytes to Co2+ and Ni2+ was similar. Some genes critically involved in the processes of inflammation and bone resorption, however, were found to be differentially regulated by these bivalent cations. The data demonstrate that monocytic gene expression is adapted in response to metal ions and that this response is, in part, specific for the individual metals. It is suggested that metal alloys used in arthroplasties may affect the extent of inflammation and bone resorption in the peri-implant tissues in dependence of their chemical composition.

Impact of viral E2-gene status on outcome after radiotherapy for patients with human papillomavirus 16-positive cancer of the uterine cervix

PURPOSE: Integration of high-risk papillomavirus DNA has been considered an important step in oncogenic progression to cervical carcinoma. Disruption of the human papillomavirus (HPV) genome within the E2 gene is frequently a consequence. This study investigated the influence of episomal viral DNA on outcome in patients with advanced cervical cancer treated with primary radiotherapy. METHODS AND MATERIALS: Paraffin-embedded biopsies of 82 women with locally advanced cervical cancer could be analyzed for HPV infection by multiplex polymerase chain reaction (PCR) by use of SPF1/2 primers. E2-gene intactness of HPV-16-positive samples was analyzed in 3 separate amplification reactions by use of the E2A, E2B, E2C primers. Statistical analyses (Kaplan-Meier method; log-rank test) were performed for overall survival (OS), disease-free survival (DFS), local progression-free survival (LPFS), and distant metastases-free survival (DMFS). RESULTS: Sixty-one (75%) of 82 carcinomas were HPV positive, 44 of them for HPV-16 (72%). Seventeen of the 44 HPV-16-positive tumors (39%) had an intact E2 gene. Patients with a HPV-16-positive tumor and an intact E2 gene showed a trend for a better DFS (58% vs. 38%, p = 0.06) compared with those with a disrupted E2 gene. A nonsignificant difference occurred regarding OS (87% vs. 66%, p = 0.16) and DMFS (57% vs. 48%, p = 0.15). CONCLUSION: E2-gene status may be a promising new target, but more studies are required to elucidate the effect of the viral E2 gene on outcome after radiotherapy in HPV-positive tumors.

A noncoding melanophilin gene (MLPH) SNP at the splice donor of exon 1 represents a candidate causal mutation for coat color dilution in dogs

Coat color dilution in several breeds of dog is characterized by a specific pigmentation phenotype and sometimes accompanied by hair loss and recurrent skin inflammation, the so-called color dilution alopecia or black hair follicular dysplasia. Coat color dilution (d) is inherited as a Mendelian autosomal recessive trait. In a previous study, MLPH polymorphisms showed perfect cosegregation with the dilute phenotype within breeds. However, different dilute haplotypes were found in different breeds, and no single polymorphism was identified in the coding sequence that was likely to be causative for the dilute phenotype. We resequenced the 5'-region of the canine MLPH gene and identified a strong candidate single nucleotide polymorphism within the nontranslated exon 1, which showed perfect association to the dilute phenotype in 65 dilute dogs from 7 different breeds. The A/G polymorphism is located at the last nucleotide of exon 1 and the mutant A-allele is predicted to reduce splicing efficiency 8-fold. An MLPH mRNA expression study using quantitative reverse transcriptase-polymerase chain reaction confirmed that dd animals had only about approximately 25% of the MLPH transcript compared with DD animals. These results provide preliminary evidence that the reported regulatory MLPH mutation might represent a causal mutation for coat color dilution in dogs.