OrgXenomics: an integrated proteomic knowledge base for patient-derived organoid and xenograft.

Journal: Nucleic acids research
PMID: 39373514

Abstract

Patient-derived models (PDMs, particularly organoids and xenografts) are irreplaceable tools for precision medicine, from target development to lead identification, then to preclinical evaluation, and finally to clinical decision-making. So far, PDM-based proteomics has emerged to be one of the cutting-edge directions and massive data have been accumulated. However, such PDM-based proteomic data have not been provided by any of the available databases, and proteomics profiles of all proteins in proteomic study are also completely absent from existing databases. Herein, an integrated database named 'OrgXenomics' was thus developed to provide the proteomic data for PDMs, which was unique in (a) explicitly describing the establishment detail for a wide array of models, (b) systematically providing the proteomic profiles (expression/function/interaction) for all proteins in studied proteomic analysis and (c) comprehensively giving the raw data for diverse organoid/xenograft-based proteomic studies of various diseases. Our OrgXenomics was expected to server as one good complement to existing proteomic databases, and had great implication for the practice of precision medicine, which could be accessed at: https://idrblab.org/orgxenomics/.

Authors

  • Yintao Zhang
    College of Pharmaceutical Sciences, Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China.
  • Xichen Lian
    College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China.
  • Hangwei Xu
    College of Pharmaceutical Sciences, Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China.
  • Sisi Zhu
    Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China.
  • Hao Zhang
    College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou, 450002, China.
  • Ziheng Ni
    Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China.
  • Tingting Fu
    School of Mechanical Engineering, Southwest Jiaotong University, Chengdu 610031, China.
  • Shuiping Liu
    Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China.
  • Lin Tao
    Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
  • Ying Zhou
    Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
  • Feng Zhu
    Department of Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China.

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