Unraveling Molecular Differences of Gastric Cancer by Label-Free Quantitative Proteomics Analysis

Int J Mol Sci. 2016 Jan 21;17(1):69. doi: 10.3390/ijms17010069.


Gastric cancer (GC) has significant morbidity and mortality worldwide and especially in China. Its molecular pathogenesis has not been thoroughly elaborated. The acknowledged biomarkers for diagnosis, prognosis, recurrence monitoring and treatment are lacking. Proteins from matched pairs of human GC and adjacent tissues were analyzed by a coupled label-free Mass Spectrometry (MS) approach, followed by functional annotation with software analysis. Nano-LC-MS/MS, quantitative real-time polymerase chain reaction (qRT-PCR), western blot and immunohistochemistry were used to validate dysregulated proteins. One hundred forty-six dysregulated proteins with more than twofold expressions were quantified, 22 of which were first reported to be relevant with GC. Most of them were involved in cancers and gastrointestinal disease. The expression of a panel of four upregulated nucleic acid binding proteins, heterogeneous nuclear ribonucleoprotein hnRNPA2B1, hnRNPD, hnRNPL and Y-box binding protein 1 (YBX-1) were validated by Nano-LC-MS/MS, qRT-PCR, western blot and immunohistochemistry assays in ten GC patients' tissues. They were located in the keynotes of a predicted interaction network and might play important roles in abnormal cell growth. The label-free quantitative proteomic approach provides a deeper understanding and novel insight into GC-related molecular changes and possible mechanisms. It also provides some potential biomarkers for clinical diagnosis.

Keywords: LC-MS/MS; Label-free quantitative proteomics; Y-box binding protein 1; gastric cancer; heterogeneous nuclear ribonucleoprotein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenocarcinoma / diagnosis
  • Adenocarcinoma / genetics*
  • Adenocarcinoma / pathology
  • Adenocarcinoma / surgery
  • Adult
  • Aged
  • Biomarkers, Tumor / genetics*
  • Gene Expression Regulation, Neoplastic*
  • Gene Regulatory Networks
  • Heterogeneous-Nuclear Ribonucleoprotein D / genetics*
  • Heterogeneous-Nuclear Ribonucleoprotein D / metabolism
  • Heterogeneous-Nuclear Ribonucleoprotein Group A-B / genetics*
  • Humans
  • Male
  • Middle Aged
  • Molecular Sequence Annotation
  • Prognosis
  • Protein Interaction Mapping
  • Proteomics / methods
  • Recurrence
  • Ribonucleoproteins / genetics*
  • Signal Transduction
  • Stomach Neoplasms / diagnosis
  • Stomach Neoplasms / genetics*
  • Stomach Neoplasms / pathology
  • Stomach Neoplasms / surgery
  • Tumor Microenvironment / genetics
  • Y-Box-Binding Protein 1 / genetics*


  • Biomarkers, Tumor
  • HNRNPL protein, human
  • Heterogeneous-Nuclear Ribonucleoprotein D
  • Heterogeneous-Nuclear Ribonucleoprotein Group A-B
  • Ribonucleoproteins
  • Y-Box-Binding Protein 1
  • YBX1 protein, human
  • hnRNP A2