Systematic Proteogenomic Approach to Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins

Keun Na, Heon Shin, Jin Young Cho, Sang Hee Jung, Jaeseung Lim, Jong Sun Lim, Eun Ah Kim, Hye Sun Kim, Ah Reum Kang, Ji Hye Kim, Jeong Min Shin, Seul Ki Jeong, Chae Yeon Kim, Jun Young Park, Hyung Min Chung, Gilbert S. Omenn, William S. Hancock, Young-Ki Paik

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to fill the knowledge gaps between human genomic information and the corresponding proteomic information. These gaps are due to "missing" proteins (MPs) - predicted proteins with insufficient evidence from mass spectrometry (MS), biochemical, structural, or antibody analyses - that currently account for 2579 of the 19587 predicted human proteins (neXtProt, 2017-01). We address some of the lessons learned from the inconsistent annotations of missing proteins in databases (DB) and demonstrate a systematic proteogenomic approach designed to explore a potential new function of a known protein. To illustrate a cautious and strategic approach for characterization of novel function in vitro and in vivo, we present the case of Na(+)/H(+) exchange regulatory cofactor 1 (NHERF1/SLC9A3R1, located at chromosome 17q25.1; hereafter NHERF1), which was mistakenly labeled as an MP in one DB (Global Proteome Machine Database; GPMDB, 2011-09 release) but was well known in another public DB and in the literature. As a first step, NHERF1 was determined by MS and immunoblotting for its molecular identity. We next investigated the potential new function of NHERF1 by carrying out the quantitative MS profiling of placental trophoblasts (PXD004723) and functional study of cytotrophoblast JEG-3 cells. We found that NHERF1 was associated with trophoblast differentiation and motility. To validate this newly found cellular function of NHERF1, we used the Caenorhabditis elegans mutant of nrfl-1 (a nematode ortholog of NHERF1), which exhibits a protruding vulva (Pvl) and egg-laying-defective phenotype, and performed genetic complementation work. The nrfl-1 mutant was almost fully rescued by the transfection of the recombinant transgenic construct that contained human NHERF1. These results suggest that NHERF1 could have a previously unknown function in pregnancy and in the development of human embryos. Our study outlines a stepwise experimental platform to explore new functions of ambiguously denoted candidate proteins and scrutinizes the mandated DB search for the selection of MPs to study in the future.

Original languageEnglish
Pages (from-to)4455-4467
Number of pages13
JournalJournal of Proteome Research
Volume16
Issue number12
DOIs
Publication statusPublished - 2017 Dec 1

Fingerprint

Trophoblasts
Databases
Proteins
Mass Spectrometry
Mass spectrometry
Proteome
Chromosomes
Protein Databases
Vulva
Caenorhabditis elegans
Human Chromosomes
Human Development
Proteogenomics
Proteomics
Immunoblotting
Embryonic Development
Transfection
Ovum
Phenotype
Pregnancy

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Chemistry(all)

Cite this

Na, Keun ; Shin, Heon ; Cho, Jin Young ; Jung, Sang Hee ; Lim, Jaeseung ; Lim, Jong Sun ; Kim, Eun Ah ; Kim, Hye Sun ; Kang, Ah Reum ; Kim, Ji Hye ; Shin, Jeong Min ; Jeong, Seul Ki ; Kim, Chae Yeon ; Park, Jun Young ; Chung, Hyung Min ; Omenn, Gilbert S. ; Hancock, William S. ; Paik, Young-Ki. / Systematic Proteogenomic Approach to Exploring a Novel Function for NHERF1 in Human Reproductive Disorder : Lessons for Exploring Missing Proteins. In: Journal of Proteome Research. 2017 ; Vol. 16, No. 12. pp. 4455-4467.
@article{d05a9b443b7c4e68a6a306d83c1187ce,
title = "Systematic Proteogenomic Approach to Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins",
abstract = "One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to fill the knowledge gaps between human genomic information and the corresponding proteomic information. These gaps are due to {"}missing{"} proteins (MPs) - predicted proteins with insufficient evidence from mass spectrometry (MS), biochemical, structural, or antibody analyses - that currently account for 2579 of the 19587 predicted human proteins (neXtProt, 2017-01). We address some of the lessons learned from the inconsistent annotations of missing proteins in databases (DB) and demonstrate a systematic proteogenomic approach designed to explore a potential new function of a known protein. To illustrate a cautious and strategic approach for characterization of novel function in vitro and in vivo, we present the case of Na(+)/H(+) exchange regulatory cofactor 1 (NHERF1/SLC9A3R1, located at chromosome 17q25.1; hereafter NHERF1), which was mistakenly labeled as an MP in one DB (Global Proteome Machine Database; GPMDB, 2011-09 release) but was well known in another public DB and in the literature. As a first step, NHERF1 was determined by MS and immunoblotting for its molecular identity. We next investigated the potential new function of NHERF1 by carrying out the quantitative MS profiling of placental trophoblasts (PXD004723) and functional study of cytotrophoblast JEG-3 cells. We found that NHERF1 was associated with trophoblast differentiation and motility. To validate this newly found cellular function of NHERF1, we used the Caenorhabditis elegans mutant of nrfl-1 (a nematode ortholog of NHERF1), which exhibits a protruding vulva (Pvl) and egg-laying-defective phenotype, and performed genetic complementation work. The nrfl-1 mutant was almost fully rescued by the transfection of the recombinant transgenic construct that contained human NHERF1. These results suggest that NHERF1 could have a previously unknown function in pregnancy and in the development of human embryos. Our study outlines a stepwise experimental platform to explore new functions of ambiguously denoted candidate proteins and scrutinizes the mandated DB search for the selection of MPs to study in the future.",
author = "Keun Na and Heon Shin and Cho, {Jin Young} and Jung, {Sang Hee} and Jaeseung Lim and Lim, {Jong Sun} and Kim, {Eun Ah} and Kim, {Hye Sun} and Kang, {Ah Reum} and Kim, {Ji Hye} and Shin, {Jeong Min} and Jeong, {Seul Ki} and Kim, {Chae Yeon} and Park, {Jun Young} and Chung, {Hyung Min} and Omenn, {Gilbert S.} and Hancock, {William S.} and Young-Ki Paik",
year = "2017",
month = "12",
day = "1",
doi = "10.1021/acs.jproteome.7b00146",
language = "English",
volume = "16",
pages = "4455--4467",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "12",

}

Na, K, Shin, H, Cho, JY, Jung, SH, Lim, J, Lim, JS, Kim, EA, Kim, HS, Kang, AR, Kim, JH, Shin, JM, Jeong, SK, Kim, CY, Park, JY, Chung, HM, Omenn, GS, Hancock, WS & Paik, Y-K 2017, 'Systematic Proteogenomic Approach to Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins', Journal of Proteome Research, vol. 16, no. 12, pp. 4455-4467. https://doi.org/10.1021/acs.jproteome.7b00146

Systematic Proteogenomic Approach to Exploring a Novel Function for NHERF1 in Human Reproductive Disorder : Lessons for Exploring Missing Proteins. / Na, Keun; Shin, Heon; Cho, Jin Young; Jung, Sang Hee; Lim, Jaeseung; Lim, Jong Sun; Kim, Eun Ah; Kim, Hye Sun; Kang, Ah Reum; Kim, Ji Hye; Shin, Jeong Min; Jeong, Seul Ki; Kim, Chae Yeon; Park, Jun Young; Chung, Hyung Min; Omenn, Gilbert S.; Hancock, William S.; Paik, Young-Ki.

In: Journal of Proteome Research, Vol. 16, No. 12, 01.12.2017, p. 4455-4467.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Systematic Proteogenomic Approach to Exploring a Novel Function for NHERF1 in Human Reproductive Disorder

T2 - Lessons for Exploring Missing Proteins

AU - Na, Keun

AU - Shin, Heon

AU - Cho, Jin Young

AU - Jung, Sang Hee

AU - Lim, Jaeseung

AU - Lim, Jong Sun

AU - Kim, Eun Ah

AU - Kim, Hye Sun

AU - Kang, Ah Reum

AU - Kim, Ji Hye

AU - Shin, Jeong Min

AU - Jeong, Seul Ki

AU - Kim, Chae Yeon

AU - Park, Jun Young

AU - Chung, Hyung Min

AU - Omenn, Gilbert S.

AU - Hancock, William S.

AU - Paik, Young-Ki

PY - 2017/12/1

Y1 - 2017/12/1

N2 - One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to fill the knowledge gaps between human genomic information and the corresponding proteomic information. These gaps are due to "missing" proteins (MPs) - predicted proteins with insufficient evidence from mass spectrometry (MS), biochemical, structural, or antibody analyses - that currently account for 2579 of the 19587 predicted human proteins (neXtProt, 2017-01). We address some of the lessons learned from the inconsistent annotations of missing proteins in databases (DB) and demonstrate a systematic proteogenomic approach designed to explore a potential new function of a known protein. To illustrate a cautious and strategic approach for characterization of novel function in vitro and in vivo, we present the case of Na(+)/H(+) exchange regulatory cofactor 1 (NHERF1/SLC9A3R1, located at chromosome 17q25.1; hereafter NHERF1), which was mistakenly labeled as an MP in one DB (Global Proteome Machine Database; GPMDB, 2011-09 release) but was well known in another public DB and in the literature. As a first step, NHERF1 was determined by MS and immunoblotting for its molecular identity. We next investigated the potential new function of NHERF1 by carrying out the quantitative MS profiling of placental trophoblasts (PXD004723) and functional study of cytotrophoblast JEG-3 cells. We found that NHERF1 was associated with trophoblast differentiation and motility. To validate this newly found cellular function of NHERF1, we used the Caenorhabditis elegans mutant of nrfl-1 (a nematode ortholog of NHERF1), which exhibits a protruding vulva (Pvl) and egg-laying-defective phenotype, and performed genetic complementation work. The nrfl-1 mutant was almost fully rescued by the transfection of the recombinant transgenic construct that contained human NHERF1. These results suggest that NHERF1 could have a previously unknown function in pregnancy and in the development of human embryos. Our study outlines a stepwise experimental platform to explore new functions of ambiguously denoted candidate proteins and scrutinizes the mandated DB search for the selection of MPs to study in the future.

AB - One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to fill the knowledge gaps between human genomic information and the corresponding proteomic information. These gaps are due to "missing" proteins (MPs) - predicted proteins with insufficient evidence from mass spectrometry (MS), biochemical, structural, or antibody analyses - that currently account for 2579 of the 19587 predicted human proteins (neXtProt, 2017-01). We address some of the lessons learned from the inconsistent annotations of missing proteins in databases (DB) and demonstrate a systematic proteogenomic approach designed to explore a potential new function of a known protein. To illustrate a cautious and strategic approach for characterization of novel function in vitro and in vivo, we present the case of Na(+)/H(+) exchange regulatory cofactor 1 (NHERF1/SLC9A3R1, located at chromosome 17q25.1; hereafter NHERF1), which was mistakenly labeled as an MP in one DB (Global Proteome Machine Database; GPMDB, 2011-09 release) but was well known in another public DB and in the literature. As a first step, NHERF1 was determined by MS and immunoblotting for its molecular identity. We next investigated the potential new function of NHERF1 by carrying out the quantitative MS profiling of placental trophoblasts (PXD004723) and functional study of cytotrophoblast JEG-3 cells. We found that NHERF1 was associated with trophoblast differentiation and motility. To validate this newly found cellular function of NHERF1, we used the Caenorhabditis elegans mutant of nrfl-1 (a nematode ortholog of NHERF1), which exhibits a protruding vulva (Pvl) and egg-laying-defective phenotype, and performed genetic complementation work. The nrfl-1 mutant was almost fully rescued by the transfection of the recombinant transgenic construct that contained human NHERF1. These results suggest that NHERF1 could have a previously unknown function in pregnancy and in the development of human embryos. Our study outlines a stepwise experimental platform to explore new functions of ambiguously denoted candidate proteins and scrutinizes the mandated DB search for the selection of MPs to study in the future.

UR - http://www.scopus.com/inward/record.url?scp=85037345412&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85037345412&partnerID=8YFLogxK

U2 - 10.1021/acs.jproteome.7b00146

DO - 10.1021/acs.jproteome.7b00146

M3 - Article

C2 - 28960081

AN - SCOPUS:85037345412

VL - 16

SP - 4455

EP - 4467

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 12

ER -