Recherche cancer
Evolution cancer
Hagenbüchle Otto, Senior scientist,  DNA array facility e-mail pdf group members
Otto Hagenbüchle was trained as biologist and received his PhD from the University of Bern in 1975. He spent the next four years as a postdoctoral fellow in the laboratories of J.A Steitz at Yale and K.U. Sprague at the University of Oregon in Eugene. He joined the group of Cellular Differentiation at ISREC as an associate scientist in 1979 and is senior scientist since 1985. In 1982 he shared the Friedrich Miescher award with U. Schibler. In 2001, he started the NCCR/ISREC DNA array facility which was integrated into the Lausanne DNA array facility in 2004 where he is responsible for the Affymetrix platform.
The Lausanne DNA array facility (DAFL)
 

In January 2004 all the activities of the NCCR DNA array facility were integrated into the DAFL located in the Center for Integrative Genomics of the University of Lausanne in Dorigny. The DAFL is headed by Dr Keith Harshman and provides in addition to the Affymetrix technology access to printed cDNA and Agilent oligonucleotide technologies. Recently the DAFL purchased a 7900HT Fast Real Time PCR System which is an excellent complement to all other technologies. This system is also going to be used for the quantitation of microRNAs, until we have figured out which commercial array system is the optimal one. We intend to implement an array-based system for the miRNA profiling and are currently testing different commercial approaches. In the future we want to apply this newly developed technology to biological systems and provide it as a new service at the DAFL.

We want to provide the users with all of the Affymetrix technologies which they need for their research. At the present time the Affymetrix platform proposes transcriptome profiling for eu‑ and prokaryotes as a service and we are in the process of introducing the 100 and 500k GeneChip technology for genotyping. The emergence of the tiling and promoter arrays will also provide the users with additional tools for analyzing gene expression. Our bioinformatician (Beate Sick) introduced an automated tool for Affymetrix data quality control and low level statistical analysis (RACE) which facilitates the early assessment of the data tremendously and helps streamlining the wet lab and data analysis processes. Over the past years we have also accumulated experience in the use of the Bioanalyzer and NanoDrop for RNA quality control (integrity and chemical purity) and have established internal rules which are helpful to guide the users in their experiments.

To keep up with the newest developments in the field, we organize monthly Chip Clubs with the users and the Lausanne Genomics Days, a two-day meeting where the invited speakers discuss their latest results. In addition we are also involved in teaching and organizing introductory courses for the students.

hTERT mRNA in blood plasma as a diagnostic tool for cancer

The discoveries of tumor-derived RNA in plasma of cancer patients and fetal-derived RNA in plasma of pregnant women have opened up a new field for studying gene expression non-invasively. Our prime target is the human Telomerase Reverse Transcriptase (hTERT) mRNA which has been shown to be over-expressed in more than 75% of tumors while most normal cells do not express this mRNA. One of the big problems is the low abundance and instability of the mRNA in the plasma which makes its detection technically difficult.

RNA has a very short half-life in plasma and in collaboration with Eclosion and Roland Sahli (CHUV), we are trying to optimize the plasma preparation and RNA extraction procedures which seem to be the critical steps to allow reproducible measurements to be made.

From published results it seems that only fragments of the mRNAs are retained in the plasma and it will be interesting to establish a map of these stable parts of the hTERT mRNA. We hope to validate this method as a non-invasive clinical diagnostic tool.

Keywords

Transcriptome profiling, Affymetrix, free plasma RNA