Identification and handling of artifactual gene expression profiles emerging in microarray hybridization experiments

Mathematical methods of analysis of microarray hybridizations deal with gene expression profiles as elementary units. However, some of these profiles do not reflect a biologically relevant transcriptional response, but rather stem from technical artifacts. Here, we describe two technically independent but rationally interconnected methods for identification of such artifactual profiles. Our diagnostics are based on detection of deviations from uniformity, which is assumed as the main underlying principle of microarray design. Method 1 is based on detection of non-uniformity of microarray distribution of printed genes that are clustered based on the similarity of their expression profiles. Method 2 is based on evaluation of the presence of gene-specific microarray spots within the slides' areas characterized by an abnormal concentration of low/high differential expression values, which we define as 'patterns of differentials'. Applying two novel algorithms, for nested clustering (method 1) and for pattern detection (method 2), we can make a dual estimation of the profile's quality for almost every printed gene. Genes with artifactual profiles detected by method 1 may then be removed from further analysis. Suspicious differential expression values detected by method 2 may be either removed or weighted according to the probabilities of patterns that cover them, thus diminishing their input in any further data analysis.

Molecular and functional evidence for early divergence of an endothelin-like system during metazoan evolution: analysis of the Cnidarian, hydra

A novel putative endothelin-converting enzyme (ECE) has been cloned from hydra, a freshwater invertebrate that belongs to the second oldest phylum of the animal kingdom. As an integral component of the endothelin system, vertebrate ECE functions in the activation of endothelin (ET) peptides. Vertebrate ETs are (1) the most potent vasoconstrictors known in mammals; and (2) function as essential signaling ligands during development of tissues derived from neural crest cells. To date, only a limited number of immunocytochemical studies have suggested the presence of endothelin-like peptides in invertebrates. Based on structural and functional analyses, we present evidence for a functional endothelin-like system in hydra that is involved in both muscle contraction and developmental processes. These findings indicate the broad use of endothelin systems in metazoans and also indicate that this type of signaling system arose early in evolution even before divergence of protostomes and deuterostomes.

Hydra metalloproteinase 1: a secreted astacin metalloproteinase whose apical axis expression is differentially regulated during head regeneration

The newly emerging astacin metalloproteinase family comprises multiple members with diverse functions. Most recently, the development-related functions have been attributed to both (1) proteolytic cleavage and subsequent release of active TGF-beta-like growth factors from latent inhibitory complexes and (2) modification of extracellular matrix (ECM) assembly and composition. We previously identified and purified hydra metalloproteinase 1 (HMP-1), a developmentally important astacin proteinase that functions in head regeneration and transdifferentiation of tentacle battery cells (L. Yan et al., 1995, Development 121, 1591-1602). In the present study, further cloning revealed that HMP-1 is produced as a secreted zymogen with a conserved hydrophobic signal sequence and a putative propeptide. The processed HMP-1 is composed of a characteristic astacin proteinase domain and a unique Cys-rich C-terminus. With this simple domain structure, HMP-1 represents an ancestral astacin proteinase. Consistent with its role in head regeneration, HMP-1 mRNA is expressed at highest levels by endodermal cells at the apical pole of the body column just inferior to the base of tentacles, the region of active cell differentiation or transdifferentiation. A modified immunocytochemical procedure demonstrated that HMP-1 protein can be localized not only to ECM of tentacles as we previously reported, but also to endodermal cells of the body column in a pattern similar to its mRNA distribution. The localization of HMP-1 protein in tentacles was confirmed using an enzymatic approach. A translocation of HMP-1 protein from cells in the body column to the extracellular milieu in tentacles further suggests that HMP-1 is a secreted protein. HMP-1 expression undergoes extensive regulation at the transcriptional level both temporally and spatially during head regeneration. The involvement of HMP-1 in this morphogenetic process is further supported by the blockage of head regeneration with localized antisense treatment. Taken together, these results suggest that HMP-1 is a secreted astacin metalloproteinase that has an important role in regulating hydra head morphogenesis potentially through its differential expression along the body axis.