Protein biomarkers for in vitro testing of toxicology

• Published in: Mutation research Vol. 746; no. 2; pp. 113 - 123
• Main Authors: Schrattenholz, André, Šoškić, Vukić, Schöpf, Rainer, Poznanović, Slobodan, Klemm-Manns, Martina, Groebe, Karlfried
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.08.2012; Elsevier BV
• Subjects: Animal Testing Alternatives - methods; Animals; Bioinformatics; Biomarkers; Biomarkers - analysis; Computational Biology; Data processing; Developmental Biology - methods; Developmental toxicity; Embryonic Stem Cells; Epigenesis, Genetic; G3BP; genomics; high-throughput screening; Humans; Infants; Integration; Legislation; Mass spectroscopy; Metabolomics; Molecular structure; Mutagenesis; Mutation; Neoplasms - chemistry; Pharmaceuticals; Post-translation; Protein biomarker; Proteins; Proteins - analysis; proteomics; Proteomics - classification; Proteomics - methods; Radioisotope labeling; Ras-GTPase-activating protein SH3-domain binding protein; Risk assessment; Statistics; Systems Biology; Toxicity; Toxicity Tests - methods; Toxicology; Toxicology - methods; Transcriptome; Translation; Validation Studies as Topic; Vision; Developmental toxicity; VPA; Radioisotope labeling; MA plot; DNMT; SNP; Protein biomarker; ESI; GC; Da; HPLC; FIA; PSA; CE; AD; Q-TOF; ANXA3; MS; EST; ROC; PARP-1; PCA; NMR; Systems biology; API; G3BP; pl; Ras-GTPase-activating protein SH3-domain binding protein; ELISA; HDAC
• ISSN: 1383-5718; 0027-5107; 1879-3592; 1873-135X
• DOI: 10.1016/j.mrgentox.2012.02.008

► Promotes the integration of molecular detail obtained by modern-omics technologies using in vitro models for toxicological research in the context of pathway-oriented toxicology. ► Discussion of the developments from nucleic acid-based high-throughput methods toward systems biology in the context of clinical translational research and personalized medicine. ► Suggestion of adapting biomarker discovery and development strategies of clinical diagnostics to toxicological research. ► Show case example: protein biomarkers for reproductive toxicology from embryonic stem cell models. The vision of the toxicology in the 21st century movement is to overcome the currently used animal tests and identify molecular pathways of toxicity, using human in vitro systems with the aim to provide the most relevant mechanistic information for human risk assessment. It is expected to translate key surrogate biomarkers to novel types of toxicity-related high throughput screening of the many thousands of compounds which need to be tested during development phases of the pharmaceutical industry and with regard to the REACH legislation in Europe. Systems biology, an emerging and increasingly popular field of research, appears to be the discipline of choice to integrate results from transcriptomics, proteomics, epigenomics and metabonomics technologies used to analyze samples from toxicological models. The challenges, however, with respect to data generation, statistical treatment, bioinformatic integration and interpretation or in silico modeling remain formidable. One of the main difficulties is the fact that the sheer number of molecular species is inflated enormously in the course of translation from genes to proteins due to post-translational modifications. Moreover, at the level of proteins, time scales of cellular reactions to toxic insults can be very fast, ranging from milliseconds to seconds. Linear dynamic ranges of concentration differences between conditions can also differ by several orders of magnitude. So, the search for protein biomarkers of toxicity requires sophisticated strategies for time-resolved quantitative differential approaches. The statistical principles, normalization of primary data and principal component and cluster analysis have been well developed for genomics/transcriptomics and partly for proteomics, but have not been widely adapted to technologies like metabonomics. Also, the integration of functional data, in particular data from mass spectrometry, with the aim of modeling pathways of toxicity for human risk assessment, is still at an infant stage.