Research fields: Molecular biology, oncogenomics, and bioinformatics

•Biomedical Research Group, Dep. of Informatics, University of Oslo, Norway
        Adjunct associate professor (equivalent førsteamanuensis II)

• Dep. of Genetics, Inst. for Cancer Research, The Norwegian Radium Hospital
        Scientist and Project Leader
• Dep. of Pathology, The Norwegian Radium Hospital, Norway
        Post-doc / Scientist (equivalent forsker)
• Dep. of Genetics, Inst. for Cancer Research, The Norwegian Radium Hospital
        Post-doc
• Div. of Molecular Biology, Dep. of Biology, University of Oslo, Norway
        Dr. scient. (equivalent PhD)
• Dep. of Biology,Albert-Ludwigs-University Freiburg, Germany
        Diploma in biology (equivalent M.Sc. or cand.scient.)
• Dep. of Botany, Trinity College Dublin, Ireland
        Exchange student in biology
• Dep. of Biology, Albert-Ludwigs-University Freiburg, Germany
        Intermediate diploma in biology (equivalent cand.mag.)
• Philosophical Faculty, Albert-Ludwigs-University Freiburg, Germany
        Philosophical studies (equivalent ex.phil.)
• Max-Planck-Gymnasium Lahr, Germany
        Abitur (equivalent school leaving examination or examen artium)

Molecular signatures of disseminated tumor cells in breast cancer

The main focus of this project group is to explore the genomic characteristics of disseminated tumor cells in breast cancer and to allocate their relevance to clinical parameters. The critical step in breast cancer progression is the establishment of metastasis to distant organs. Circulating tumor cells (CTC) in peripheral blood and disseminated tumor cells (DTC) in secondary organs like bone marrow are considered to be rare members among the cellular population of primary tumor cells. In several studies it has been demonstrated that the presence of these cells is an independent prognostic factor and detection of DTC identifies patients with less favorable clinical outcome. However, we still lack knowledge of the genomic characteristics of DTC and how to target these cells. A reason for this limitation has been a deficiency of procedures allowing high-resolution analyses of CTC/DTC, including DNA-copy number changes. Due to the implementation of a state-of-the-art technique, called single cell array comparative genomic hybridization (SCaCGH), we are finally able to perform in-depth analysis of occult circulating tumor cells on various high density array platforms. Further, new tools for detection and characterization of CTC/DTC including qRT-PCR have been developed. Genotyping and phenotyping of occult tumor cells will provide information to better understand tumor initiation, tumor heterogeneity, and subsequent metastasis formation. Using novel bioinformatic and biostatistical tools studied in connection with a detailed primary tumor analysis, we wish to identify biological markers and genes responsible for the capacity of cancer cells to metastasize. This may be clinically useful as evidence for an early occult spread of tumor cells, as a relevant prognostic factor, and finally, permit direct exploration of markers for targeted treatment.

The project is an integrative part of the Breast Cancer study in the Micrometastasis project ongoing at the Norwegian Radium Hospital. The work is performed in close collaboration between the Dep. of Pathology and the Dep. of Genetics.

The project is supported by DISMAL. The main objective of DISMAL is to improve specificity and sensitivity of current platforms for DTC (disseminated tumor cells) detection in patients with epithelial tumors. The Goal is to identify novel markers at the DNA, RNA or protein level that allows a more precise detection of DTC with a high risk for metastatic progression.

This project resulted in the following publications:

Further information to this project

Prosjektbeskrivelse på norsk

The aim of this subproject is to a) establish, evaluate and possibly develop new bioinformatical tools to handle the massive data obtained from microarray experiments to compare gene expression- with gene copy number data from classical and various array based CGH analyses. b)Identify and characterize genes that are dysregulated by other mechanisms than copy number alterations. c) Analyze the impact of the above identified genes(or gene clusters) on clinical parameters and patient outcome d) Analyze experimentally the role of mRNA binding proteins using CRD-BP and MYC genes as a model system, and search for similar protein motifs and investigate their role in breast tumorigenesis. Microarray-based Comparative Genome Hybridization (array CGH) provides the possibility to connect DNA copy-aberrations with genomic map positions. Different types of arrays may be used in such analyses, cDNA, BAC arrays containing genomic DNA or oligoarrays.In close collaboration with the Bioinformatics group, Institute of Informatics (University of Oslo), UCSF and the Stanford University a comparative study of the different methods is performed based on state-of-the-art statistical modeling and analysis methods. This project is supported by FUGE.

Unconventional gene regulation in human breast tumors

The biological dogma of a simple genetic flow of information from DNA via RNA to protein expression is on its way to disband. A manifold picture of a comprehensive and interactive regulatory system with multiple regulatory mechanisms is evolving, including non-coding RNAs, infrastructural RNAs and alternative splicing processes. Signaling proteins, RNA processing and RNA binding are frequent signals in the targeting of chromatin complexes and in the regulation of gene expression during differentiation and development. A common feature for all these regulation mechanisms is a partial or complete independence of consistency to gene copy numbers. Such uncommon regulatory features can be identified by utilizing microarray datasets, where microarray comparative genomic hybridization (array CGH) analysis of copy number variation has been performed in parallel with microarray gene expression studies. For this applied bioinformatics approach we employ the CGH-Explorer program (Lingjærde et al., 2005) in connection to additional databases, like the Extended Alternatively Spliced EST Database (EASED) and others. In a first attempt we concentrated on RNA binding proteins. Particularly, the IMPs (Insulin-like growth factor II mRNA-binding Proteins) have been investigated, a highly conserved family of RNA binding proteins, all containing 4 KH (K protein Homologous) and 2 RRMs (RNA Recognition Motifs) domains. IMPs are expressed in development and tumorgenesis, e.g. IMP1 protects myc from endonucleolytic degradation by binding to its instability coding region. To determine the role of IMPs in human breast tumors real-time quantitative PCR assay were performed with 60 tumors samples from patients with locally advanced disease (Geisler et al., (2001), Cancer Research 61, 2505). Several IMPs show significant correlation to different clinical parameters. The growing list of unconventional gene regulation mechanisms is striking and we hypothesize that many of them are present and dysregulated in cancer. This seems to be not only to be an interesting feature for cancer diagnostic and therapeutic issues but also for the biological understanding of the mechanisms of gene regulating as such.

This project resulted in the following publications:

Further information to this project

Prosjektbeskrivelse på norsk

Identification and analysis of genes controlling embryogenesis and embryo dormancy in plants

Prior to germination mature seeds in many higher plants undergo a period of dormancy. The dormancy stage is characterised by the temporary failure to immediately germinate under favourable conditions until specific environmental stimuli, like low temperature (stratification) and light, release this inhibition. In this thesis an attempt has been taken to form a better understanding of the genes and processes controlling embryogenesis and dormancy in plants. In screenings of EMS-mutagenized and T-DNA tagged lines several INSOMNIAC (nsm) mutants were identified that rapidly germinate in light without prior stratification. Mutants in NSM1 and NSM2 are dominant alleles; mutants at the NSM5 locus are semi-dominant alleles with an age-dependent level of penetrance. NSM1, NSM2 and NSM5 are necessary for the repression of precocious germination of immature seed in culture but not for the inhibition of vivipary. Seeds of nsm1 and nsm2 have wild-type sensitivity to abscisic acid (ABA), in contrast to the ABA-hypersensitivity of nsm5 seeds. However, all nsm mutant plants have normal vegetative and reproductive growth. Mapping of NSM genes was performed using PCR-based protocols. Several critical parameters of the standard method needed to be modified in order to provide a reliable and efficient mapping technique, including increased density of markers for various Arabidopsis ecotypes. NSM1, NSM2 and NSM5 were mapped to different loci on chromosome 5. To study the establishment, maintenance and release of dormancy the mRNA levels of LEC1, FUS3 and ABI3 were examined in various strong or moderate dormancy ecotypes and the nsm1, nsm2 and nsm5-1 and abi3-1 mutants. Observed marginal variations in mRNA levels of the various markers show no obvious correlation to differences in dormancy levels. Analysis of ABI3, AtEm1 and AtEm6 expression in Ws wild-type and nsm mutant seeds exposed to variable conditions of light, temperature and afterripening revealed reduced AtEm1 and AtEm6 and altered ABI3 mRNA levels in nsm mutants. However, changes due to temperature and light factors are similar to those that occur in Ws wild-type seeds. An alternative approach performed to identify embryogenesis regulators is survey of candidate genes. In this respect SET domain genes, demonstrated to be multifunctional chromatin regulators, have been examined in the Arabidopsis genome. 37 AtSET domain genes have been identified of which at least 29 are functional genes, mainly expressed in buds, flowers and seeds. The expression patterns and the high numbers of SET domain proteins in Arabidopsis may reflect their complex regulatory role in plant development and a putative function in the process of dormancy.

This thesis resulted in the following publications:

Prosjektbeskrivelse på norsk

The influence of ozone and UV-B on the antioxidative system of spruce (Picea abies L.) under natural and controlled conditions

Erhöhte Ozonkonzentrationen und erhöhte UV-B Strahlung gelten als Auslöser für die verstärkte Bildung von Sauerstoffradikalen und damit als Ursache für oxidativen Streß. Um den Einfluß von Ozon und UV-B auf das antioxidative System von Fichten (Picea abies L.) zu bestimmen, wurden Freilanduntersuchungen Experimenten unter kontrollierten Bedingungen gegenüber gestellt. Die Reaktionen des antioxidativen Systems von verschiedenen Klonfichten und Bäumen des natürlichen Bestands auf natürliche Streßbedingungen wurden längs eines Höhengradienten (800 m - 1750 m ü. NN) am Wank untersucht und mit den Effekten einer erhöhten Ozonkonzentration in Kombination mit einer moderaten UV-B Applikation verglichen (die einfache Ozonkonzentration und die Klimabedingungen des Kammerversuchs entsprachen den an der Wank Mittelstation aufgezeichneten Werten). Eine mögliche induktive Wirkung einer kurzzeitigen UV-B Bestrahlung auf das antioxidative System, die Superoxid-dismutase-Aktivität und das Wachstum von Fichtenkeimlingen wurde in einem Keimlings-versuch untersucht. Dazu wurden 10 Wochen alte Keimlinge 0 - 4 h einer UV-B Strahlung von 6,3 MED h-1 ausgesetzt. Die klimatischen und edaphischen Bedingungen in der Hochlage bewirkten im Vergleich zur Tallage eine Streßreaktion der Klone, die sich in einer Reduktion des Frischgewicht /Trockengewicht Verhältnisses, einer Abnahme des Gesamtproteingehaltes und einer drastischen Verminderung der Chlorophyll- und Carotinoidgehalte der Nadeln verdeutlichte. Trotz dieser eindeutigen Streßsymptome veränderten sich die Malondialdehydgehalte nicht. Daher erwies sich der Malondialdehydgehalt der ein Maß für Lipidoxidationen ist, als unzureichender Streß-parameter. Weiterhin war in den Nadeln das Ascorbat Redox Verhältnis auf 70 % abgesunken und die Superoxiddismutase-Aktivität in der Hochlage im Vergleich zur des antioxidativen Systems an die Umweltbedingungen der Hochlage. Die Unterschiede in den Reaktionen des antioxidativen Systems verschiedener Klone auf die natürlichen Streßbedingungen in der Hochlage waren insgesamt nur geringfügig. Der Klon C 5/1/16 mit dem Vitalitätsmerkmal „gut“ besaß einen signifikant höheren Glutathiongehalt als die Klone C 5/1/16 und C 4/4/8 mit den Vitalitätsmerkmalen „schlecht“ und „mittel“. Da die Bäume des natürlichen Bestandes in der Hochlage einen vergleichbar hohen Glutathiongehalt aufwiesen wie der vitalste Klon, scheinen erhöhte Glutathiongehalte ein Indikator für die Adaptation an Höhenstreß zu sein. Durch die kurzzeitige UV-B Bestrahlung von Keimlingen nahm der Gehalt an Glutathion in den Primärnadeln ab, während andere Komponenten des antioxidativen Systems unbeeinflußt waren. Daraus läßt sich schließen, daß der Glutathion-gehalt sehr empfindlich auf Veränderung der Umwelt reagiert. Eine Erhöhung der Ozonkonzentration in Kammerversuchen bewirkte eine Induktion des antioxidativen Systems der Fichten. Dies resultierte in erhöhten Ascorbat- und Glutathion-gehalten. Eine Kombination von erhöhtem Ozon und moderater UV-B Strahlung schwächte diese Induktion leicht ab. Die Superoxiddismutase-Aktivität wurde durch eine Erhöhung der Ozonkonzentration nicht verändert; jedoch bewirkte die UV-B Applikation eine signifikante Erhöhung der Superoxiddismutase-Aktivität um 43 %. Eine gelelektrophoretische Trennung der Isoenzyme zeigte, daß das Isoenzymmuster bei den verschiedenen Behandlungs-varianten nicht verändert war. Von den 3 aufgetrennten Isoenzymen konnten die chloroplastidäre SOD I und die cytosolische SOD II identifiziert werden. Eine kurzfristige UV-B Bestrahlung hatte weder einen induktiven noch einen destruktiven Effekt auf das antioxidative System und das Wachstum von Fichtenkeimlingen. In den Primär-nadeln der Keimlinge wurden erhöhte Chlorophyll- und Carotinoidgehalte bestimmt, die Ascorbatgehalte und die Superoxiddismutase-Aktivität waren gegenüber den Kontrollen nicht verändert. Die Erhöhung der Superoxiddismutase-Aktivität durch die Applikation von UV-B bei dem Expositionsversuch scheint daher auf eine längerfristige Adaptation zurückzuführen zu sein. Bei Freilanduntersuchungen wurden Schadsymptome und Streßreaktionen an Nadeln der Bäume in der Hochlage beobachtet. Jedoch zeigten Versuche in Expositionskammern, daß das antioxidativen Systems auf erhöhtes Ozon und moderates UV-B mit einer Induktion reagierte. Ein induktiver UV-B Kurzzeiteffekt auf das antioxidativen Systems konnte ausgeschlossen werden. Im Freiland waren andere Schad- und Streßsymptome aufgetreten, als unter kontrollierten Bedingungen. Diese Ergebnisse lassen den Schluß zu, daß die Belastung des antioxidativen Systems, wie sie in der Hochlage beobachtet wurden, nicht allein durch eine Erhöhung der Ozonkonzentration und der UV-B Strahlung ausgelöst sein können. Weitere Umweltfaktoren wie niedrige Temperaturen und geringe Niederschläge sollten daher bei zukünftigen Untersuchungen ebenfalls berücksichtigt werden.

This thesis resulted in the following publications: