Multi-tissue proteogenomic analysis for mechanistic toxicology studies in non-model species

Area of Science:

• Genomics and Proteomics
• Regulatory Science
• Ecotoxicology

Background:

• New Approach Methodologies (NAMs) integrate omics and in vitro techniques for 3R strategies in regulatory science.
• Validating and revising complex fish genomes is crucial for accurate risk assessment.

Purpose of the Study:

• To present an integrative transcriptomics and proteomics workflow for fish genome validation and revision.
• To demonstrate the utility of proteogenomics for multi-level omics data integration in non-model species.
• To support the development and application of NAMs in regulatory and ecotoxicological studies.

Main Methods:

• Constructed proteogenomic databases using Atlantic salmon transcriptomic and LC-MS/MS data.
• Integrated publicly available transcriptomic data with in-house generated RNA-Seq and LC-MS/MS data.
• Developed proteogenomic expression matrices for analyzing tissue-specific gene expression.

Main Results:

• Identified ~80,000 peptides, confirming translation for over 40,000 RefSeq structures.
• Corrected annotations, supported novel genes, and identified unannotated genes through 183 co-located peptide groups.
• Revealed distinct tissue-specific expression profiles and homologous xenobiotic defense protein expression between in vivo and in vitro liver systems.

Conclusions:

• Proteogenomic analysis enhances understanding of complex fish genomes.
• The developed bioinformatic toolkit supports NAMs for regulatory science and ecotoxicology.
• This approach is valuable for non-model species research and risk assessment.