Thomas A McCloskey et al. (2004) West Coast Worm Meeting "Suppression of CED-3-Independent Programmed Cell Death In C. elegans"

Thomas A McCloskey, Peter Bowers, Ambuj Singh, Chiou-Wei Tsai, Joel Rothman, Vebjorn Ljosa

[West Coast Worm Meeting, 2004]

Programmed cell death (PCD) is a well conserved, genetically controlled process of cell suicide that occurs naturally during the life span of many organisms. Among the core molecular components that mediate apoptosis in C. elegans , the caspase CED-3 is a necessary activator of nearly all developmental PCD. Strong ced-3(-) mutants show nearly no PCD and all cells that would normally die instead develop, differentiate, and integrate into the host organism's tissues. Despite extensive knowledge of the core cell death machinery, the pathways that mediate this event downstream of, or in parallel to, CED-3 are not clearly defined. Debilitating the function of the apoptotic suppressor ICD-1 (Bloss et al., Nature 424: 1066 (2003)) results in widespread cell death, which, like developmental PCD, requires the essential cell death activator CED-4. However, this apoptotic death does not require CED-3 activity. Based on these observations, we performed an RNAi screen for additional suppressors of ced-3 -independent PCD which has revealed a set of ~130 candidate genes. Our investigation of these newly identified apoptotic suppressor candidates consists of three principal objectives: (1) We are currently categorizing the newly identified genes into genetic and phenotypic groups to establish classes of PCD repression. Genetic interactions with the core PCD machinery are being examined by performing candidate gene RNAi on ced-3(-) and ced-4(-) mutants. (2) We are applying Bayesian networking methods of bioinformatics to predict functional networks through which these genes may act in the organism. (3) Based on these studies, we are developing a refined list of prominent candidates that we intend to pursue by detailed mechanistic studies.

Chao-I Chen et al. (2004) West Coast Worm Meeting "A Bayesian approach toward analyzing the network of genes involved in C. elegans programmed cell death"

Chao-I Chen, Vebjorn Ljosa, S Rao Jammalamadaka, Chiou-Wei Tsai, Ambuj K Singh, Thomas A McCloskey, Xiaofang Lei, Joel H Rothman

[West Coast Worm Meeting, 2004]

From an RNAi screen for genes that repress apoptosis, we have identified a set of about 130 candidates (see abstract by McCloskey et al.). We are using computational methods in an effort to predict functional networks through which these genes may act and to identify additional candidates and their relationships within the postulated networks. We are initially working with a number of datasets as the basis for our predictions: microarray expression data, the physical orientation of genes within the worm genome, phylogenetic profile data, and PSORT predictions of protein localization. The datasets are normalized according to their overlap with the worm interactome and Wormbase subcellular localization data. They are then combined using a nave Bayesian network, to yield a set of potential functionally interacting protein pairs along with a likelihood score for each pair. Finally, we construct network maps of the protein pairs that fall above a desired likelihood ratio. Our initial efforts suggest a cluster of functional interactions that are predicted from the gene set identified by the RNAi screen; refinements of the computational methods are in progress.