title: Label-free quantitative proteomics of CD133-positive liver cancer stem cells.
abstract: BACKGROUND
  CD133-positive liver cancer stem cells, which are characterized by their resistance to conventional chemotherapy and their tumor initiation ability at limited dilutions, have been recognized as a critical target in liver cancer therapeutics. In the current work, we developed a label-free quantitative method to investigate the proteome of CD133-positive liver cancer stem cells for the purpose of identifying unique biomarkers that can be utilized for targeting liver cancer stem cells. Label-free quantitation was performed in combination with ID-based Elution time Alignment by Linear regression Quantitation (IDEAL-Q) and MaxQuant.
  
  
  RESULTS
  Initially, IDEAL-Q analysis revealed that 151 proteins were differentially expressed in the CD133-positive hepatoma cells when compared with CD133-negative cells. We then analyzed these 151 differentially expressed proteins by MaxQuant software and identified 10 significantly up-regulated proteins. The results were further validated by RT-PCR, western blot, flow cytometry or immunofluorescent staining which revealed that prominin-1, annexin A1, annexin A3, transgelin, creatine kinase B, vimentin, and EpCAM were indeed highly expressed in the CD133-positive hepatoma cells.
  
  
  CONCLUSIONS
  These findings confirmed that mass spectrometry-based label-free quantitative proteomics can be used to gain insights into liver cancer stem cells.
authors.affiliation: Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, Taiwan. cnshen@gate.sinica.edu.tw.
authors.forename: Sheng-Ta
authors.initials: ST
authors.lastname: Tsai
authors.forename: Chih-Chiang
authors.initials: CC
authors.lastname: Tsou
authors.forename: Wan-Yu
authors.initials: WY
authors.lastname: Mao
authors.forename: Wei-Chao
authors.initials: WC
authors.lastname: Chang
authors.forename: Hsin-Ying
authors.initials: HY
authors.lastname: Han
authors.forename: Wen-Lian
authors.initials: WL
authors.lastname: Hsu
authors.forename: Chung-Leung
authors.initials: CL
authors.lastname: Li
authors.forename: Chia-Ning
authors.initials: CN
authors.lastname: Shen
authors.forename: Chung-Hsuan
authors.initials: CH
authors.lastname: Chen