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Biomedical subjects

Wolfgang Raffelsberger

Publications and source records attributed to Wolfgang Raffelsberger.

3 recordsLinked to original sources

Retinoic acid determines life span of leukemic cells by inducing antagonistic apoptosis-regulatory programs.

As a single signal, retinoids induce terminal differentiation. This implies that they activate differentiation and apoptosis in a temporally defined order to allow expression of the differentiated phenotype well before death. We report that two apparently contradictory retinoid-induced programs have the capacity to define cellular life span. Anti-apoptotic factors are activated concomitantly with differentiation, while retinoids induce at the same time also pro-apoptotic signaling. We have assessed the roles of two key factors, Bcl2A1 and TRAIL, in the temporal programming of cell death and differentiation. We demonstrate that PLB985 are type II cells in which TRAIL induces apoptosis through the extrinsic and--via Bid activation--also the intrinsic death pathways. Bcl2A1, ectopically over-expressed, or endogenously induced by retinoic acid receptor agonists, protected cells from apoptosis triggered by TRAIL, whose induction required the activation of both the retinoic acid and retinoid X receptors. Bcl2A1 prevented loss of mitochondrial membrane potential and caspase-9, but not caspase-8, activation. The expression of anti-sense Bcl2A1 sensitized PLB985 cells to TRAIL. Co-culture experiments revealed protection from fraternicide if sister cells were pre-exposed to retinoic acid. Collectively, our data support a model in which retinoids orchestrate a life span-regulatory program comprising Bcl2A1 induction to temporally protect against concomitantly induced TRAIL death signaling. Termination of this life span in presence of Bcl2A1 is most likely a consequence of the Bid-independent TRAIL action. Thus, depending on the retinoic acid and retinoid X receptor activation potential of a ligand and the relative efficacies of the intrinsic and extrinsic death pathways in a given cell, a single retinoid triggers the life span of a differentiated phenotype.

Apoptosis↗

Density of points clustering, application to transcriptomic data analysis.

With the increasing amount of data produced by high-throughput technologies in many fields of science, clustering has become an integral step in exploratory data analysis in order to group similar elements into classes. However, many clustering algorithms can only work properly if aided by human expertise. For example, one parameter which is crucial and often manually set is the number of clusters present in the analyzed set. We present a novel stopping rule to find the optimal number of clusters based on the comparison of the density of points inside the clusters and between them. The method is evaluated on synthetic as well as on real transcriptomic data and compared with two current methods. Finally, we illustrate its usefulness in the analysis of the expression profiles of promyelocytic cells before and after treatment with all-trans retinoic acid. Simultaneous clustering for gene regulation and absolute initial expression levels allowed the identification of numerous genes associated with signal transduction revealing the complexity of retinoic acid signaling.

Algorithms↗

Quality indicators increase the reliability of microarray data.

Large-scale gene expression profiling with DNA microarrays opens new dimensions to molecular biology but still lacks the overall precision of traditional low-scale techniques. We developed a novel strategy of data processing linking search stringency to quality indicators for efficient detection of low-level, regulated genes. Using retinoid-induced differentiation of NB-4 promyelocytic cells, the variation of expression profiles between biological duplicates was studied and compared with the changes induced by all-trans retinoic acid (atRA) treatment. An analysis of 4320 genes showed that retinoic acid has mainly geneactivating function in NB-4 cells. Treatment with atRA for 18 hours induced metabolic genes that may be associated with cell differentiation and signaling factors triggering later events leading to apoptosis; cytokine genes were among the highest stimulated by atRA. Notably, we identified a regulatory loop inhibiting MYC action: as MYC was downregulated, a cognate repressor of MYC was upregulated.

Cluster Analysis↗