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Paik YK, Lane L, Kawamura T, Chen YJ, Cho JY, LaBaer J, Yoo JS, Domont G, Corrales F, Omenn GS, Archakov A, Encarnación-Guevara S, Lui S, Salekdeh GH, Cho JY, Kim CY, Overall CM. Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. J Proteome Res 2018; 17:4042-4050. [PMID: 30269496 PMCID: PMC6693327 DOI: 10.1021/acs.jproteome.8b00383] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An important goal of the Human Proteome Organization (HUPO) Chromosome-centric Human Proteome Project (C-HPP) is to correctly define the number of canonical proteins encoded by their cognate open reading frames on each chromosome in the human genome. When identified with high confidence of protein evidence (PE), such proteins are termed PE1 proteins in the online database resource, neXtProt. However, proteins that have not been identified unequivocally at the protein level but that have other evidence suggestive of their existence (PE2-4) are termed missing proteins (MPs). The number of MPs has been reduced from 5511 in 2012 to 2186 in 2018 (neXtProt 2018-01-17 release). Although the annotation of the human proteome has made significant progress, the "parts list" alone does not inform function. Indeed, 1937 proteins representing ∼10% of the human proteome have no function either annotated from experimental characterization or predicted by homology to other proteins. Specifically, these 1937 "dark proteins" of the so-called dark proteome are composed of 1260 functionally uncharacterized but identified PE1 proteins, designated as uPE1, plus 677 MPs from categories PE2-PE4, which also have no known or predicted function and are termed uMPs. At the HUPO-2017 Annual Meeting, the C-HPP officially adopted the uPE1 pilot initiative, with 14 participating international teams later committing to demonstrate the feasibility of the functional characterization of large numbers of dark proteins (CP), starting first with 50 uPE1 proteins, in a stepwise chromosome-centric organizational manner. The second aim of the feasibility phase to characterize protein (CP) functions of 50 uPE1 proteins, termed the neXt-CP50 initiative, is to utilize a variety of approaches and workflows according to individual team expertise, interest, and resources so as to enable the C-HPP to recommend experimentally proven workflows to the proteome community within 3 years. The results from this pilot will not only be the cornerstone of a larger characterization initiative but also enhance understanding of the human proteome and integrated cellular networks for the discovery of new mechanisms of pathology, mechanistically informative biomarkers, and rational drug targets.
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Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center and Department of Integrative Omics, Yonsei University, Sudaemoon-ku, Seoul, Korea
| | - Lydie Lane
- CALIPHO group, Swiss Institute of Bioinformatics & Department of Microbiology and Molecular medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Takeshi Kawamura
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0032 Japan
| | - Yu-Ju Chen
- Institute of Chemistry Academia Sinica, 128 Academia Road Sec. 2, Nankang Taipei 115 Taiwan
| | - Je-Yoel Cho
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul University, 1 Gwanak-, Gwanak-gu, 151-742 Seoul, South Korea
| | - Joshua LaBaer
- McAllister Ave. Arizona State University, Tempe, Arizona, 85287-5001, USA
| | - Jong Shin Yoo
- Division of Mass Spectrometry Research, Korea Basic Science Institute, Ochang, Korea
| | - Gilberto Domont
- Federal University of Rio de Janeiro Institute of Chemistry, Rio de Janeiro, RJ Brazil
| | - Fernando Corrales
- Functional Proteomics Laboratory National Center of Biotechnology, CSIC 28049 Madrid, Spain
| | - Gilbert S. Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | | | | | - Siqi Lui
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, 1665659911, Tehran, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Jin-Young Cho
- Yonsei Proteome Research Center and Department of Integrative Omics, Yonsei University, Sudaemoon-ku, Seoul, Korea
| | - Chae-Yeon Kim
- Yonsei Proteome Research Center and Department of Integrative Omics, Yonsei University, Sudaemoon-ku, Seoul, Korea
| | - Christopher M. Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
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