Comparative proteomics, network analysis and post-translational modification identification reveal differential profiles of plasma Con A-bound glycoprotein biomarkers in gastric cancer

Yih Huei Uen; Kai Yuan Lin; Ding Ping Sun; Chen Chung Liao; Ming-Song Hsieh; Yung Kai Huang; Yen Wei Chen; Pei Hsuan Huang; Wei Jung Chen; Chih Chun Tai; Kuan Wei Lee; You Chia Chen; Ching Yu Lin

doi:10.1016/j.jprot.2013.03.007

Comparative proteomics, network analysis and post-translational modification identification reveal differential profiles of plasma Con A-bound glycoprotein biomarkers in gastric cancer

Yih Huei Uen, Kai Yuan Lin, Ding Ping Sun, Chen Chung Liao, Ming-Song Hsieh, Yung Kai Huang, Yen Wei Chen, Pei Hsuan Huang, Wei Jung Chen, Chih Chun Tai, Kuan Wei Lee, You Chia Chen, Ching Yu Lin

Research output: Contribution to journal › Article › peer-review

51 Citations (Scopus)

Abstract

In the study, we used Con A affinity chromatography, 1-D gel electrophoresis, and nano-LC-MS/MS to screen biomarker candidates in plasma samples obtained from 30 patients with gastric cancer and 30 healthy volunteers. First, we pooled plasma samples matched by age and sex. We identified 17 differentially expressed Con A-bound glycoproteins, including 10 upregulated proteins and 7 downregulated proteins; these differences were significant (Student's t-test, p-value41, trimethylation at aspartic acid-²⁹⁰, and flavin adenine dinucleotide at histidine-³³⁵. Biological significanceOur study was to describe a combinatorial approach of Con A affinity chromatography, 1-D SDS-PAGE, and nano-LC/MS/MS that provides a label-free, comparative glycoproteomic quantification strategy for the investigation of glycoprotein profiles in plasma from gastric cancer patients versus healthy volunteers and to identify glycoprotein biomarkers for the early clinical detection of gastric cancer. Three novel PTMs, HexHexNAc, trimethylation and FAD, in Con A-bound ITIH3 were identified and built in molecular modeling. The aspartic acid-²⁹⁰ trimethylation site was located in a metal ion-dependent adhesion site (MIDAS motif; ²⁹⁰-DXSXS. .T. .D-³¹³) that may influence important function for binding protein ligands.

Original language	English
Pages (from-to)	197-213
Number of pages	17
Journal	Journal of Proteomics
Volume	83
DOIs	https://doi.org/10.1016/j.jprot.2013.03.007
Publication status	Published - May 7 2013

Keywords

Concanavalin A
Gastric cancer
Glycoproteins
Human plasma
Mass spectrometry
Post-translational modification

ASJC Scopus subject areas

Biophysics
Biochemistry

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.jprot.2013.03.007

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Uen, Y. H., Lin, K. Y., Sun, D. P., Liao, C. C., Hsieh, M-S., Huang, Y. K., Chen, Y. W., Huang, P. H., Chen, W. J., Tai, C. C., Lee, K. W., Chen, Y. C., & Lin, C. Y. (2013). Comparative proteomics, network analysis and post-translational modification identification reveal differential profiles of plasma Con A-bound glycoprotein biomarkers in gastric cancer. Journal of Proteomics, 83, 197-213. https://doi.org/10.1016/j.jprot.2013.03.007

Uen, YH, Lin, KY, Sun, DP, Liao, CC, Hsieh, M-S, Huang, YK, Chen, YW, Huang, PH, Chen, WJ, Tai, CC, Lee, KW, Chen, YC & Lin, CY 2013, 'Comparative proteomics, network analysis and post-translational modification identification reveal differential profiles of plasma Con A-bound glycoprotein biomarkers in gastric cancer', Journal of Proteomics, vol. 83, pp. 197-213. https://doi.org/10.1016/j.jprot.2013.03.007

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title = "Comparative proteomics, network analysis and post-translational modification identification reveal differential profiles of plasma Con A-bound glycoprotein biomarkers in gastric cancer",

abstract = "In the study, we used Con A affinity chromatography, 1-D gel electrophoresis, and nano-LC-MS/MS to screen biomarker candidates in plasma samples obtained from 30 patients with gastric cancer and 30 healthy volunteers. First, we pooled plasma samples matched by age and sex. We identified 17 differentially expressed Con A-bound glycoproteins, including 10 upregulated proteins and 7 downregulated proteins; these differences were significant (Student's t-test, p-value41, trimethylation at aspartic acid-290, and flavin adenine dinucleotide at histidine-335. Biological significanceOur study was to describe a combinatorial approach of Con A affinity chromatography, 1-D SDS-PAGE, and nano-LC/MS/MS that provides a label-free, comparative glycoproteomic quantification strategy for the investigation of glycoprotein profiles in plasma from gastric cancer patients versus healthy volunteers and to identify glycoprotein biomarkers for the early clinical detection of gastric cancer. Three novel PTMs, HexHexNAc, trimethylation and FAD, in Con A-bound ITIH3 were identified and built in molecular modeling. The aspartic acid-290 trimethylation site was located in a metal ion-dependent adhesion site (MIDAS motif; 290-DXSXS. .T. .D-313) that may influence important function for binding protein ligands.",

keywords = "Concanavalin A, Gastric cancer, Glycoproteins, Human plasma, Mass spectrometry, Post-translational modification",

author = "Uen, {Yih Huei} and Lin, {Kai Yuan} and Sun, {Ding Ping} and Liao, {Chen Chung} and Ming-Song Hsieh and Huang, {Yung Kai} and Chen, {Yen Wei} and Huang, {Pei Hsuan} and Chen, {Wei Jung} and Tai, {Chih Chun} and Lee, {Kuan Wei} and Chen, {You Chia} and Lin, {Ching Yu}",

note = "Funding Information: We thank Professor Yuan-Chii Lee for the discussions regarding the IPA analysis. This study was supported by grant 99CM-TMU-12 from the Foundation of Chi Mei Medical Center and grant NSC101-2622-B-038-001-CC3 from the National Science Council in Taiwan. ",

year = "2013",

month = may,

day = "7",

doi = "10.1016/j.jprot.2013.03.007",

language = "English",

volume = "83",

pages = "197--213",

journal = "Journal of Proteomics",

issn = "1874-3919",

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TY - JOUR

T1 - Comparative proteomics, network analysis and post-translational modification identification reveal differential profiles of plasma Con A-bound glycoprotein biomarkers in gastric cancer

AU - Uen, Yih Huei

AU - Lin, Kai Yuan

AU - Sun, Ding Ping

AU - Liao, Chen Chung

AU - Hsieh, Ming-Song

AU - Huang, Yung Kai

AU - Chen, Yen Wei

AU - Huang, Pei Hsuan

AU - Chen, Wei Jung

AU - Tai, Chih Chun

AU - Lee, Kuan Wei

AU - Chen, You Chia

AU - Lin, Ching Yu

N1 - Funding Information: We thank Professor Yuan-Chii Lee for the discussions regarding the IPA analysis. This study was supported by grant 99CM-TMU-12 from the Foundation of Chi Mei Medical Center and grant NSC101-2622-B-038-001-CC3 from the National Science Council in Taiwan.

PY - 2013/5/7

Y1 - 2013/5/7

N2 - In the study, we used Con A affinity chromatography, 1-D gel electrophoresis, and nano-LC-MS/MS to screen biomarker candidates in plasma samples obtained from 30 patients with gastric cancer and 30 healthy volunteers. First, we pooled plasma samples matched by age and sex. We identified 17 differentially expressed Con A-bound glycoproteins, including 10 upregulated proteins and 7 downregulated proteins; these differences were significant (Student's t-test, p-value41, trimethylation at aspartic acid-290, and flavin adenine dinucleotide at histidine-335. Biological significanceOur study was to describe a combinatorial approach of Con A affinity chromatography, 1-D SDS-PAGE, and nano-LC/MS/MS that provides a label-free, comparative glycoproteomic quantification strategy for the investigation of glycoprotein profiles in plasma from gastric cancer patients versus healthy volunteers and to identify glycoprotein biomarkers for the early clinical detection of gastric cancer. Three novel PTMs, HexHexNAc, trimethylation and FAD, in Con A-bound ITIH3 were identified and built in molecular modeling. The aspartic acid-290 trimethylation site was located in a metal ion-dependent adhesion site (MIDAS motif; 290-DXSXS. .T. .D-313) that may influence important function for binding protein ligands.

AB - In the study, we used Con A affinity chromatography, 1-D gel electrophoresis, and nano-LC-MS/MS to screen biomarker candidates in plasma samples obtained from 30 patients with gastric cancer and 30 healthy volunteers. First, we pooled plasma samples matched by age and sex. We identified 17 differentially expressed Con A-bound glycoproteins, including 10 upregulated proteins and 7 downregulated proteins; these differences were significant (Student's t-test, p-value41, trimethylation at aspartic acid-290, and flavin adenine dinucleotide at histidine-335. Biological significanceOur study was to describe a combinatorial approach of Con A affinity chromatography, 1-D SDS-PAGE, and nano-LC/MS/MS that provides a label-free, comparative glycoproteomic quantification strategy for the investigation of glycoprotein profiles in plasma from gastric cancer patients versus healthy volunteers and to identify glycoprotein biomarkers for the early clinical detection of gastric cancer. Three novel PTMs, HexHexNAc, trimethylation and FAD, in Con A-bound ITIH3 were identified and built in molecular modeling. The aspartic acid-290 trimethylation site was located in a metal ion-dependent adhesion site (MIDAS motif; 290-DXSXS. .T. .D-313) that may influence important function for binding protein ligands.

KW - Concanavalin A

KW - Gastric cancer

KW - Glycoproteins

KW - Human plasma

KW - Mass spectrometry

KW - Post-translational modification

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DO - 10.1016/j.jprot.2013.03.007

M3 - Article

C2 - 23541716

AN - SCOPUS:84876716480

SN - 1874-3919

VL - 83

SP - 197

EP - 213

JO - Journal of Proteomics

JF - Journal of Proteomics

ER -

Comparative proteomics, network analysis and post-translational modification identification reveal differential profiles of plasma Con A-bound glycoprotein biomarkers in gastric cancer

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

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