Project ZET-O-MAP

Development of an analysis pipeline to identify biomarkers for developmental toxicity

The zebrafish embryo toxicity assay (ZET) was originally developed for environmental biomonitoring (von Hellfeld et al., 2020: The possibility it provides to observe numerous morphological changes occurring during zebrafish embryo development in the first five days furthermore makes it a suitable model for studying developmental toxicity (Beker van Woudenberg et al., 2013:

© Fraunhofer ITEM
By combining morphological data with transcriptome data, researchers are seeking to identify biomarkers for particular morphological changes.

With the aim of identifying specific biomarkers for teratogenic effects at developmental stages, Fraunhofer ITEM researchers have developed an analysis pipeline in the CEFIC-LRI project ZET-O-MAP that links morphological changes with alterations in gene expression. For this purpose, they set up a database that pools and harmonizes data on morphological changes from published ZETs. In addition, they compiled transcriptome data from public sources such as GeneExpressionOmnibus (GEO) and reprocessed these using a uniform analysis approach. To supplement the data found, three test substances were additionally tested in concentration series in the ZET over five days and samples for RNA sequencing were taken at four different developmental stages of the embryos. For these substances, as well as for those with comparable data quality, it is possible to determine time-resolved biomarkers in addition to morphological changes. This analytical approach is in line with the overall requirements for regulatory use (Verheijen et al., 2022:, enabling robust and comparable results. The combination of morphological data and transcriptome data allows the identification of biomarkers for particular morphological changes. In the next step, the data will be used to either substantiate or refute the read-across hypothesis for already established substance groups.

Your contact person

Sylvia Escher

Contact Press / Media

Dr. Sylvia Escher

Head of Department of In-silico Toxicology

Phone +49 511 5350-330