BioProject

Modeled on human connectivity mapping (Cmap), this study was undertaken to investigate the potential applications of Cmap approach in ecotoxicology. More...

Modeled on human connectivity mapping (Cmap), this study was undertaken to investigate the potential applications of Cmap approach in ecotoxicology. Over 3500 zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) transcriptomic profiles, each associated with one of several dozen chemical treatment conditions, were compiled into three distinct collections of rank-ordered gene lists (ROGLs) by species and microarray platforms. Individual query signatures, each consisting of multiple gene probes differentially expressed in a chemical condition, were used to interrogate the reference ROGLs. Informative connections were established at high success rates within species when, as defined by their mechanisms of action (MOAs), both query signatures and ROGLs were associated with the same or similar chemicals. In other words, a simple query signature functioned effectively as an exposure biomarker, without going through a typical time-consuming process of development and validation. More importantly, a large reference database of ROGLs also enabled a query signature to cross- interrogate other chemical conditions with overlapping MOAs, leading to novel groupings and subgroupings of seemingly unrelated chemicals at a finer resolution. This approach confirmed the identities of several estrogenic chemicals, as well as a polycyclic aromatic hydrocarbon and a neuro-toxin, in the largely uncharacterized water samples near several waste water treatment plants, and thus demonstrates its future potential in real world applications. The power of Cmap should grow along with the chemical coverage of its ROGLs, making it a framework easily scalable in the future. For toxicity extrapolation across fish species, however, a sufficient number of GEPs linked to chemical conditions common to multiple fish species are needed next in order to conduct a more thorough feasibility study of interspecific Cmap. Overall design: total RNA from the ovary tissue of treated or control fish labeled in single color was hybridized to Agilent fathead minnow microarray (design 019597, 036574) Less...