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Functional Genomics of Brain Development and Developmentally Related Brain Disease in Drosophila

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Functional genomics of brain development and developmentally related brain disease in Drosophila Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Thomas Loop aus Deutschland Basel 2004 Zoologisches Institut der Universität Basel Pharmazentrum Klingelbergstrasse 50 CH-4056 Basel Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Heinrich Reichert und Prof. Dr. Karl-Friedrich Fischbach. Basel, den 21.09.2004 Prof. Dr. Marcel Tanner - 2 - Contents 1. Summary........................................................................................................................................................- 4 - 2. Introduction...................................................................................................................................................- 6 - 2.1. Drosophila as a model system ...............................................................................................................- 6 - 2.2. The development of the Drosophila brain...........................................................................................- 6 - 2.2.1. The Drosophila neuroblasts........................................................................................................- 10 - 2.2.2. Gliogenesis in Drosophila............................................................................................................- 11 - 2.2.3. Patterning the brain via the otd and the homeotic genes .........................................................- 14 - 2.2.4. The three phases of neurogenesis ...............................................................................................- 15 - 2.3. The Drosophila genome and high density oligonucleotide arrays ...................................................- 15 - 2.4. Drosophila as a model in cancer research .........................................................................................- 18 - 2.4.1. The brain tumor gene acts as a tumor suppressor in Drosophila............................................- 19 - 2.6. Scope of this thesis...............................................................................................................................- 21 - 3. Quantitative transcript imaging in normal and heat shocked Drosophila embryos using high-density oligonucleotide arrays.....................................................................................................................................- 23 - 4. Identification of candidate downstream genes for the homeodomain transcription factor Labial in Drosophila through oligonucleotide array transcript imaging....................................................................- 40 - 5. Functional Equivalence of Hox Gene Products in the Specification of the Tritocerebrum during Embryonic Brain Development of Drosophila..............................................................................................- 60 - 6. Evolutionary conservation of otd/Otx2 transcription factor action: a genome-wide microarray analysis in Drosophila....................................................................................................................................................- 82 - 7. Gliogenesis in Drosophila: Genome-Wide Analysis of Downstream Genes of glial cells missing in the Embryonic Nervous System .........................................................................................................................- 111 - 8. Transcriptional signature of an adult brain tumor in Drosophila ........................................................- 140 - 9. Discussion...................................................................................................................................................- 181 - Functional equivalence of hometic proteins and Labial target genes ..................................................- 181 - Glial cells missing and regulation of neurogliogenesis...........................................................................- 182 - Evolutionary conservation of Otd/Otx transcription factors ...............................................................- 183 - Transcriptional profile of an adult Drosophila tumor...........................................................................- 184 - Genome-wide transcript profiling in Drosophila brain development ..................................................- 188 - 10. References................................................................................................................................................- 193 - Acknowledgements........................................................................................................................................- 202 - - 3 - 1. Summary One of the fundamental challenges in basic neuroscience is to understand the molecular genetic networks associated with building the brain. As malfunction in these genetic pathways can lead to disorders like cancer, brain development is also a crucial research area for clinical neuroscience. In the course of this thesis, different molecular aspects of Drosophila brain development and related neoplastic disease were analyzed using high- density oligonucleotide arrays. The homeotic selector gene labial (lab) plays an important role in specification of neuronal identity in the embryonic brain of Drosophila. In labial mutants presumptive neurons in the posterior tritocerebrum fail to differentiate. This leads to severe defects in tritocerebral axon pathways. Using high density oligonucleotide arrays we identified downstream target genes of Labial and showed that only a limited and distinct set of genes expressed in the embryo is regulated by this homeoprotein. Furthermore, we performed genetic rescue experiments to analyze the functional equivalence of Drosophila Hox gene products in specification of the tritocerebral neuromere. Surprisingly, all tested homeotic proteins, with the exception of Abd-B, were able to rescue the labial mutant phenotype in the tritocerebrum. These results indicate that the specificity of homeotic gene action in embryonic brain development has to be modulated by cis-acting regulatory elements. Another study circled around the homeobox transcription factor otd and its human homolog Otx2. Cross-phylum rescue experiments have shown that these genes are functionally equivalent. We used quantitative transcript imaging to analyze otd and Otx gene action in the Drosophila embryo at a genomic level. Our experiments suggest that about one third of the Otd-regulated transcripts in Drosophila can also be controlled by the human Otx2. These common otd/Otx2 downstream genes are likely to represent the molecular basis for the functional equivalence of otd and Otx2 gene action in Drosophila. glial cells missing (gcm) is a key control gene of gliogenesis. gcm loss-of-function leads to a transformation of glial cells into neurons and, conversely, when gcm is ectopically misexpressed, presumptive neurons become glia. Since gcm encodes a transcription factor it is supposed that a set of downstream genes are regulated by GCM that in turn execute the glial differentiation program. Again, a set of full-genome transcript profiling experiments was conducted to identify gcm downstream genes in a comprehensive manner. A set of several hundred candidate gcm target genes were identified in this screen, giving new insights into neuroglial fate specification in Drosophila. Brain tumors have been extensively studied by looking at genetic alterations and mutations that lead to malignant growth. Still, the causes of brain tumorigenesis are largely unknown. Model systems like Drosophila can be of great help to shed light on altered transcriptional activity in brain tumor phenotypes. To investigate the in vivo transcriptional activity associated with a brain tumor, we conducted genome-wide microarray expression analyses of an adult brain tumor in Drosophila caused by homozygous mutation in the tumor suppressor gene brain tumor (brat). Two independent gene expression studies using two different oligonucleotide - 4 - microarray platforms were used to compare the transcriptome of adult wildtype flies with mutants displaying the adult bratk06028 mutant brain tumor. Cross-validation and stringent statistical criteria identified a core transcriptional signature of bratk06028 neoplastic tissue. We found highly significant expression level changes for 321 annotated genes associated with the adult neoplastic bratk06028 tissue indicating elevated and aberrant metabolic and cell cycle activity, upregulation of the basal transcriptional machinery, as well as elevated and aberrant activity of ribosome synthesis and translation control. One fifth of these genes show homology to known mammalian genes involved in cancer formation. These results identify for the first time the genome-wide transcriptional alterations associated with an adult brain tumor in Drosophila and reveal insights into the possible mechanisms of tumor formation caused by homozygous mutation of the translational repressor brat. - 5 - 2. Introduction 2.1. Drosophila as a model system Drosophila melanogaster has been an important genetic model system for nearly one hundred years. The wealth of genetic, molecular and transgenic tools available today, combined with a short lifecycle of the species and low maintenance cost makes it a superior system to answer a wide variety of biological
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