Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function

Young Ki Paik, Lydie Lane, Takeshi Kawamura, Yu Ju Chen, Je Yoel Cho, Joshua LaBaer, Jong Shin Yoo, Gilberto Domont, Fernando Corrales, Gilbert S. Omenn, Alexander Archakov, Sergio Encarnación-Guevara, Siqi Lui, Ghasem Hosseini Salekdeh, Jin Young Cho, Chae Yeon Kim, Christopher M. Overall

Research output: Contribution to journalReview article

13 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)4042-4050
Number of pages9
JournalJournal of Proteome Research
Volume17
Issue number12
DOIs
StatePublished - Dec 7 2018

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Human Chromosomes
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Workflow
Biomarkers
Pathology
Human Genome

Keywords

  • C-HPP
  • dark protein
  • Human Proteome Project
  • missing protein
  • neXt-CP50
  • protein evidence
  • proteoform
  • uncharacterized missing protein (uMP)
  • uncharacterized protein evidence 1 (uPE1)

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. / Paik, Young Ki; Lane, Lydie; Kawamura, Takeshi; Chen, Yu Ju; Cho, Je Yoel; LaBaer, Joshua; Yoo, Jong Shin; Domont, Gilberto; Corrales, Fernando; Omenn, Gilbert S.; Archakov, Alexander; Encarnación-Guevara, Sergio; Lui, Siqi; Salekdeh, Ghasem Hosseini; Cho, Jin Young; Kim, Chae Yeon; Overall, Christopher M.

In: Journal of Proteome Research, Vol. 17, No. 12, 07.12.2018, p. 4042-4050.

Research output: Contribution to journalReview article

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 2018, 'Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function', Journal of Proteome Research, vol. 17, no. 12, pp. 4042-4050. https://doi.org/10.1021/acs.jproteome.8b00383
Paik, Young Ki ; Lane, Lydie ; Kawamura, Takeshi ; Chen, Yu Ju ; Cho, Je Yoel ; LaBaer, Joshua ; Yoo, Jong Shin ; Domont, Gilberto ; Corrales, Fernando ; Omenn, Gilbert S. ; Archakov, Alexander ; Encarnación-Guevara, Sergio ; Lui, Siqi ; Salekdeh, Ghasem Hosseini ; Cho, Jin Young ; Kim, Chae Yeon ; Overall, Christopher M. / Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. In: Journal of Proteome Research. 2018 ; Vol. 17, No. 12. pp. 4042-4050.
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AU - Cho, Je Yoel

AU - LaBaer, Joshua

AU - Yoo, Jong Shin

AU - Domont, Gilberto

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AU - Omenn, Gilbert S.

AU - Archakov, Alexander

AU - Encarnación-Guevara, Sergio

AU - Lui, Siqi

AU - Salekdeh, Ghasem Hosseini

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AU - Kim, Chae Yeon

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