Label-free quantitative proteomics of CD133-positive liver cancer stem cells
1 Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, Taiwan
2 Genomics Research Center, Academia Sinica, Taipei, Taiwan
3 Institute of Information Science, Academia Sinica, Taipei, Taiwan
4 Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
5 Department of Chemistry, National Taiwan University, Taipei, Taiwan
6 Institute of Atomic & Molecular Sciences, Academia Sinica, Taipei, Taiwan
Proteome Science 2012, 10:69 doi:10.1186/1477-5956-10-69Published: 21 November 2012
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.
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.
These findings confirmed that mass spectrometry-based label-free quantitative proteomics can be used to gain insights into liver cancer stem cells.