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

• Published in: Frontiers in cell and developmental biology Vol. 7; p. 299
• Main Authors: Chen, Geng, Chen, Jiwei, Liu, Huanlong, Chen, Shuangguan, Zhang, Yang, Li, Peng, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Mattes, William, Ning, Baitang, Shi, Tieliu
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 21-11-2019
• Subjects: Cell and Developmental Biology; human secretome; proteome; RNA-seq; secreted proteins; transcriptome; secreted proteins; RNA-seq; human secretome; transcriptome; proteome
• ISSN: 2296-634X; 2296-634X
• DOI: 10.3389/fcell.2019.00299

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.