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  3. Proteomics-based multi-omics identifies the roadmap of transcription-translation-protein dynamics in planarian regeneration

Proteomics-based multi-omics identifies the roadmap of transcription-translation-protein dynamics in planarian regeneration

  • Dev Cell. 2025 Sep 16:S1534-5807(25)00536-2. doi: 10.1016/j.devcel.2025.08.015.
Yuqing Ying 1,  Yuanyi Zhou Xiong 2,  Xue Pan 1,  Qiushi Zhang 3,  Jiajia Chen 1,  Yun Zhao 4,  Xue Cai 5,  Xiao Yi 3,  Yi Zhu 5,  Tiannan Guo 6,  Kai Lei 7
Affiliations

Affiliations

  • 1 College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
  • 2 Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Fudan University, Shanghai, China.
  • 3 Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, Zhejiang, China.
  • 4 Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Fudan University, Shanghai, China.
  • 5 iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
  • 6 iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China. Electronic address: guotiannan@westlake.edu.cn.
  • 7 Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China. Electronic address: leikai@westlake.edu.cn.
PMID: 40961932 DOI: 10.1016/j.devcel.2025.08.015
Abstract

Identifying regulators for tissue regeneration is fundamental for regenerative biology. While transcription dynamics control planarian regeneration initiation, how protein machinery controls regeneration remains unclear, as transcript levels often fail to predict protein abundance. To address this gap, we performed mass-spectrometry-based proteomic analyses of the planarian Schmidtea mediterranea, establishing a spectral library covering ∼10,000 proteins, and employed quantitative approaches to measure proteome dynamics during regeneration. Our study identified upregulated ribosomal proteins, which were supported by ribosome profiling Sequencing (Ribo-seq). Combining RNA Sequencing (RNA-seq) and Ribo-seq analyses categorized the increased protein abundance into regulatory modes at transcriptional, translational, and protein stability levels. Functional examination identified 25 proteins essential for planarian regeneration. Troponin T was identified as a regulator of regeneration initiation, showing increased protein abundance before upregulation at transcriptional and translational levels, suggesting a regulation of protein stability. In summary, our study demonstrates previously unexplored ribosome-mediated and transcription-independent protein machinery essential for planarian regeneration initiation.

Keywords

DIA; Ribo-seq; TMT; blastema; post-transcriptional regulation; proteomics; regeneration; ribosome; troponin complex; wound response.

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