Large-scale, quantitative proteomics reveals key proteins required for planarian regeneration initiation

Multi-omics studies are increasingly used to decipher the mechanisms underlying tissue regeneration. However, the use of proteomics for such studies has been limited due to the high cost and relatively low throughput and reproducibility. The genes required for planarian regeneration have primarily been identified based on changes in mRNA transcripts; previous studies have not addressed the possibility of protein upregulation prior to detectable increases in transcript abundance during the early stages of planarian regeneration. Here, we used in-depth high-throughput proteomics approaches to analyze the model planarian Schmidtea mediterranea during regeneration and discovered 13 proteins that are essential regulators of key regeneration steps. Two of these proteins, Troponin T and MRPL18, are key regulators of regeneration initiation and showed increases in protein abundance prior to upregulation at the mRNA level. Extensive comparisons between proteomic and transcriptomic datasets suggested the critical mechanisms beyond the transcriptional level, such as the translational and post-translational levels. In summary, this study revealed key regulators of regeneration in a model organism; furthermore, it established an adaptable spectral library and comprehensive proteomics datasets, enabling future in-depth and multi-omics analyses of planarian biology. Overall design: mRNA of planarians three days post lethal irradiation treatment vs wide type control