Abstract Introduction: Cancer stem cells (CSC) have been increasingly recognized as playing a major role in various fields of breast tumor biology including carcinogeneis, metastasis and resistance to cytotoxic drugs and radiotherapy. Identification of protein biomarkers associated with breast CSC may help understanding CSC biology as well as identifying novel diagnostics and specific therapeutic targets. 2-D Fluorescence Difference Gel Electrophoresis (2-D DIGE) is a method that labels protein samples with fluorescent dyes before 2-D electrophoresis, enabling accurate analysis of differences in protein abundance between samples. Methods: Using flow cytometry-based ALDEFLUOR assay (ALD), we isolated CSC-enriched (ALD-positive) and non CSC-enriched (ALD-negative) cell populations of MDA-MB-453, a human breast cancer cell line. Total proteins were extracted from both fractions using urea-based buffer and subjected to 2D-DIGE. Differentially expressed spots were excised, proteins were gel-extracted, digested and identified using MALDI-TOF MS (Ultraflex, Brucker Daltonics, Billerica, USA) Results: 2D-DIGE revealed differential expression of various protein spots between ALD-positive and ALD-negative MDA-MB-453 cells. MALDI-TOF MS analysis allowed identification of 11 differentially expressed proteins, among which 7 were down-regulated and 4 were up-regulated in ALD-positive MDA-MB-453 cells, including Poly (ADP-ribose) polymerase-1 (PARP-1). Overexpression of PARP-1 in MDA-MB-453 cells was further confirmed by western blot using specific monoclonal antibody and such an observation was extended to 4 additional human breast cancer cell lines including HCC1937, MDA-MB-436, SUM149 and SUM159. These 5 human breast cancer cells were found to display a limited short-term sensitivity (within the micromolar range) to olaparib, a specific PARP-1 inhibitor. However, a negative correlation was found between the level of overexpression and the ability of olaparib to inhibit the growth of ALD-positive cells. Conclusion: A proteomic-based approach revealed that PARP-1 was up-regulated in ALD-positive, CSC-enriched from various human breast cancer cell lines. Such an overexpression may contribute to clinical resistance to PARP-inhibitors. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-04-07.