Frontiers in Cell and Developmental Biology (Nov 2019)

Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data

  • Geng Chen,
  • Jiwei Chen,
  • Huanlong Liu,
  • Shuangguan Chen,
  • Yang Zhang,
  • Peng Li,
  • Danielle Thierry-Mieg,
  • Jean Thierry-Mieg,
  • William Mattes,
  • Baitang Ning,
  • Tieliu Shi

DOI
https://doi.org/10.3389/fcell.2019.00299
Journal volume & issue
Vol. 7

Abstract

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Secreted proteins (SPs) play important roles in diverse important biological processes; however, a comprehensive and high-quality list of human SPs is still lacking. Here we identified 6,943 high-confidence human SPs (3,522 of them are novel) based on 330,427 human proteins derived from databases of UniProt, Ensembl, AceView, and RefSeq. Notably, 6,267 of 6,943 (90.3%) SPs have the supporting evidences from a large amount of mass spectrometry (MS) and RNA-seq data. We found that the SPs were broadly expressed in diverse tissues as well as human body fluid, and a significant portion of them exhibited tissue-specific expression. Moreover, 14 cancer-specific SPs that their expression levels were significantly associated with the patients’ survival of eight different tumors were identified, which could be potential prognostic biomarkers. Strikingly, 89.21% of 6,943 SPs (2,927 novel SPs) contain known protein domains. Those novel SPs we mainly enriched with the known domains regarding immunity, such as Immunoglobulin V-set and C1-set domain. Specifically, we constructed a user-friendly and freely accessible database, SPRomeDB (www.unimd.org/SPRomeDB), to catalog those SPs. Our comprehensive SP identification and characterization gain insights into human secretome and provide valuable resource for future researches.

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