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Stefan Tomiuk

Publications and source records attributed to Stefan Tomiuk.

5 recordsLinked to original sources
PubMed2006

Comparative transcriptional and functional profiling of clear cell and papillary renal cell carcinoma.

Renal cell carcinoma (RCC) is known to effectively prevent immune recognition. However, little is known about the mechanisms that underlie this phenomenon. Thus, the identification of immunogenic molecules associated with RCC and the elucidation of the corresponding signaling pathways are crucial to the development of effective treatments. We performed transcriptional and functional profiling with cDNA microarrays (1070 cDNA probes) on a total of 17 RCCs, 11 clear cell and 6 papillary, and on corresponding normal tissue. Samples were clustered based on their expression profiles. We found a total of 45 genes to be regulated equally by both tumor types compared to the normal tissue. A set of 13 differentially expressed genes was identified between the examined tumor subtypes. Functional analysis was performed for both gene sets and showed a significant enrichment of cell surface genes regulated in both tumor subtypes. Within these we found five surface marker genes to be upregulated (TNFRSF10B, CD70, TNFR1, PDGFRB, and BAFF) which are involved in immune responses via the regulation of lymphocytes and can also induce apoptosis. Their overexpression in both tumor subtypes suggests a possible involvement in the immune escape strategies of RCC. The combination of transcriptional and functional profiling revealed potential target molecules for novel therapy strategies that must be studied in more detail.

Carcinoma, Papillary↗
PubMed2004

Purification of neuronal precursors from the adult mouse brain: comprehensive gene expression analysis provides new insights into the control of cell migration, differentiation, and homeostasis.

The progeny of neural stem cells in the subventricular zone (SVZ) of the adult mammalian brain consists in polysialylated NCAM-expressing immature neurons (PSA(+) cells), which migrate to the olfactory bulb (OB) to differentiate into GABAergic interneurons. We purified murine PSA(+) cells directly from the adult brain by FACS and analyzed their gene expression profile by SAGE. Comparative analyses led to the identification of precursor-enriched genes, including Survivin, Sox-4, Meis2, Dishevelled-2, C3aR1 and Riken 3110003A17, and many so far uncharacterized transcripts. Cluster analysis showed that groups of genes involved in axon guidance and gene clusters implicated in chemotaxis are strongly upregulated, indicating a role of both cues in the control of cell migration in the adult brain. Furthermore, genes involved in apoptosis and cell proliferation are co-expressed, suggesting that the amount of precursors that is present in the adult brain is a result of an equilibrium of these processes.

Animals↗
PubMed2003

Elucidation of ataxin-3 and ataxin-7 function by integrative bioinformatics.

The spinocerebellar ataxias (SCAs) are a class of hereditary neurodegenerative diseases, which are caused by the pathological expansion of unstable CAG triplet repeats found in a number of apparently unrelated genes. The proteins encoded by the SCA genes typically translate this expanded (CAG)n repeat into an expanded poly(Q) stretch. Several pathological features are common to all SCAs, irrespective of the gene harbouring the expansion. The specific contributions of the mutated genes are currently hard to assess, as the physiological role of most of the so-called ataxins is not known. By combining the results of profile-based sequence analysis with genome-wide functional data available for model organisms, we have derived detailed predictions of the physiological function of two SCA gene products. Ataxin-3, the protein mutated in Machado Joseph Disease (SCA3), belongs to a novel group of cysteine-proteases and is predicted to be active against ubiquitin chains or related substrates. The catalytic site of this enzyme class is similar to that found in UBP and UCH type ubiquitin proteases. For ataxin-7, the gene product of the SCA7 gene, we have identified an orthology relationship to the yeast open reading frame Ygl066c. Recently published evidence from genome-wide studies suggests that Ygl066c is a component of the SAGA histone acetyltransferase complex. By analogy, a similar role for the mammalian ataxin-7 can be expected. The functional predictions reported here are sufficiently precise to allow a direct experimental verification. Moreover, both findings have implications for the general pathogenesis of spinocerebellar ataxias by providing a direct connection of these diseases with ubiquitin metabolism and histone acetylation.

Acetylation↗
PubMed2002

A common protein interaction domain links two recently identified epilepsy genes.

Until recently, all genes found to be mutated in hereditary idiopathic epilepsies encoded subunits of ion channels, leading to the view of this class of diseases as channelopathies. Two apparent exceptions to this rule are the MASS1 gene, which is mutated in the Frings mouse model of audiogenic epilepsy, and the LGI1 gene, which is mutated in autosomal dominant partial epilepsy with auditory features (ADPEAF). Careful sequence analysis of the two protein products encoded by those genes shows a common feature: both sequences harbour a novel homology domain consisting of a 7-fold repeated 44-residue motif. The architecture and structural features of this new domain make it a likely member of the growing class of protein interaction domains with a seven-bladed beta-propeller fold. In the MASS1 gene product, which has recently been shown to be a fragment of the very large G-protein-coupled receptor VLGR1, this EAR domain (for epilepsy-associated repeat) is part of the ligand-binding ectodomain. LGI1, as well as a number of newly identified LGI1 relatives, is predicted to be a secreted protein, and consists of an N-terminal leucine-rich repeat region and a C-terminal EAR region. The known portion of the human genome encodes six EAR proteins, some of which map to chromosome regions associated with seizure disorders. The EAR domain is likely to play an important role in the pathogenesis of epilepsy, either by binding to an unknown anti-epileptic ligand, or more likely by interfering with axon guidance or synaptogenesis.

Amino Acid Sequence↗