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1.  Mass spectrometry (LC-MS/MS) identified proteomic biosignatures of breast cancer in proximal fluid 
Journal of proteome research  2012;11(10):5034-5045.
Summary
We have begun an early phase of biomarker discovery in three clinically important types of breast cancer using a panel of human cell lines: HER2 positive, HER2 negative and hormone receptor positive and triple negative (HER2−, ER−, PR−). We identified and characterized the most abundant secreted, sloughed, or leaked proteins released into serum free media from these breast cancer cell lines using a combination of protein fractionation methods before LC-MS/MS mass spectrometry analysis. A total of 249 proteins were detected in the proximal fluid of 7 breast cancer cell lines. The expression of a selected group of high abundance and/or breast cancer specific potential biomarkers including thromobospondin 1, galectin-3 binding protein, cathepsin D, vimentin, zinc-α2-glycoprotein, CD44, and EGFR from the breast cancer cell lines and in their culture media were further validated by Western blot analysis. Interestingly, mass spectrometry identified a cathepsin D protein single-nucleotide polymorphism (SNP) by alanine to valine replacement from the MCF-7 breast cancer cell line. Comparison of each cell line media proteome displayed unique and consistent biosignatures regardless of the individual group classifications demonstrating the potential for stratification of breast cancer. Based on the cell line media proteome, predictive Tree software was able to categorize each cell line as HER2 positive, HER2 negative and hormone receptor positive and triple negative based on only two proteins, muscle fructose 1,6-bisphosphate aldolase and keratin 19. In addition, the predictive Tree software clearly identified MCF-7 cell line overexpresing the HER2 receptor with the SNP cathepsin D biomarker.
doi:10.1021/pr300606e
PMCID: PMC3521600  PMID: 22934887
breast cancer; biomarkers; blood assay; proteomics; mass spectrometry; single-nucleotide polymorphism (SNP); HER2; triple negative; proximal fluid
2.  Higher Levels of GATA3 Predict Better Survival in Women with Breast Cancer 
Human pathology  2010;41(12):1794-1801.
The GATA family members are zinc finger transcription factors involved in cell differentiation and proliferation. GATA3 in particular is necessary for mammary gland maturation, and its loss has been implicated in breast cancer development. Our goal was to validate the ability of GATA3 expression to predict survival in breast cancer patients. Protein expression of GATA3 was analyzed on a high density tissue microarray consisting of 242 cases of breast cancer. We associated GATA3 expression with patient outcomes and clinicopathological variables. Expression of GATA3 was significantly increased in breast cancer, in situ lesions, and hyperplastic tissue compared to normal breast tissue. GATA3 expression decreased with increasing tumor grade. Low GATA3 expression was a significant predictor of disease-related death in all patients, as well as in subgroups of estrogen receptor positive or low grade patients. Additionally, low GATA3 expression correlated with increased tumor size and estrogen and progesterone receptor negativity. GATA3 is an important predictor of disease outcome in breast cancer patients. This finding has been validated in a diverse set of populations. Thus, GATA3 expression has utility as a prognostic indicator in breast cancer.
doi:10.1016/j.humpath.2010.06.010
PMCID: PMC2983489  PMID: 21078439
Tissue microarray; breast cancer; tumor marker; prognostic marker
3.  Proteomic-Based Biosignatures in Breast Cancer Classification and Prediction of Therapeutic Response 
Protein-based markers that classify tumor subtypes and predict therapeutic response would be clinically useful in guiding patient treatment. We investigated the LC-MS/MS-identified protein biosignatures in 39 baseline breast cancer specimens including 28 HER2-positive and 11 triple-negative (TNBC) tumors. Twenty proteins were found to correctly classify all HER2 positive and 7 of the 11 TNBC tumors. Among them, galectin-3-binding protein and ALDH1A1 were found preferentially elevated in TNBC, whereas CK19, transferrin, transketolase, and thymosin β4 and β10 were elevated in HER2-positive cancers. In addition, several proteins such as enolase, vimentin, peroxiredoxin 5, Hsp 70, periostin precursor, RhoA, cathepsin D preproprotein, and annexin 1 were found to be associated with the tumor responses to treatment within each subtype. The MS-based proteomic findings appear promising in guiding tumor classification and predicting response. When sufficiently validated, some of these candidate protein markers could have great potential in improving breast cancer treatment.
doi:10.1155/2011/896476
PMCID: PMC3202144  PMID: 22110952
4.  Management Options in Triple-Negative Breast Cancer 
Notorious for its poor prognosis and aggressive nature, triple-negative breast cancer (TNBC) is a heterogeneous disease entity. The nature of its biological specificity, which is similar to basal-like cancers, tumors arising in BRCA1 mutation carriers, and claudin-low cancers, is currently being explored in hopes of finding the targets for novel biologics and chemotherapeutic agents. In this review, we aim to give a broad overview of the disease’s nomenclature and epidemiology, as well as the basic mechanisms of emerging targeted therapies and their performance in clinical trials to date.
doi:10.4137/BCBCR.S6562
PMCID: PMC3153117  PMID: 21863131
triple-negative breast cancer; basal-like; targeted therapy
5.  Hydrophobic Proteome Analysis of Triple Negative and Hormone-Receptor-Positive-Her2-Negative Breast Cancer by Mass Spectrometer 
Clinical Proteomics  2010;6(3):93-103.
Introduction
It is widely believed that discovery of specific, sensitive, and reliable tumor biomarkers can improve the treatment of cancer. Currently, there are no obvious targets that can be used in treating triple-negative breast cancer (TNBC).
Methods
To better understand TNBC and find potential biomarkers for targeted treatment, we combined a novel hydrophobic fractionation protocol with mass spectrometry LTQ-orbitrap to explore and compare the hydrophobic sub-proteome of TNBC with another subtype of breast cancer, hormone-receptor-positive-Her2-negative breast cancer (non-TNBC).
Results
Hydrophobic sub-proteome of breast cancer is rich in membrane proteins. Hundreds of proteins with various defined key cellular functions were identified from TNBC and non-TNBC tumors. In this study, protein profiles of TNBC and non-TNBC were systematically examined, compared, and validated. We have found that nine keratins are down-regulated and several heat shock proteins are up-regulated in TNBC tissues. Our study may provide insights of molecules that are responsible for the aggressiveness of TNBC.
Conclusion
The initial results obtained using a combination of hydrophobic fractionation and nano-LC mass spectrometry analysis of these proteins appear promising in the discovery of potential cancer biomarkers and bio-signatures. When sufficiently refined, this approach may prove useful in improving breast cancer treatment.
doi:10.1007/s12014-010-9052-1
PMCID: PMC2937135  PMID: 20930921
Hydrophobic fractionation; Cancer biomarker; Mass spectrometry; Triple-negative breast cancer; Hormone-receptor-positive-Her2-negative breast cancer
6.  Mass spectrometry (LC-MS/MS) site-mapping of N-glycosylated membrane proteins for breast cancer biomarkers 
Journal of proteome research  2009;8(8):4151-4160.
Cancer cell membrane proteins are released into the plasma/serum by exterior protein cleavage, membrane sloughing, cellular secretion or cell lysis, and represent promising candidates for interrogation. Because many known disease biomarkers are both glycoproteins and membrane bound, we chose the hydrazide method to specifically target, enrich, and identify glycosylated proteins from breast cancer cell membrane fractions using the LTQ Orbitrap mass spectrometer. Our initial goal was to select membrane proteins from breast cancer cell lines and then to use the hydrazide method to identify the N-linked proteome as a prelude to evaluation of plasma/serum proteins from cancer patients. A combination of steps facilitated identification of the glycopeptides and also defined the glycosylation sites. In MCF-7, MDA-MB-453 and MDA-MB-468 cell membrane fractions, use of the hydrazide method facilitated an initial enrichment and site mapping of 27 N-linked glycosylation sites in 25 different proteins. However, only three N-linked glycosylated proteins, galectin-3 binding protein, lysosome associated membrane glycoprotein 1, and oxygen regulated protein, were identified in all three breast cancer cell lines. In addition, MCF-7 cells shared an additional 3 proteins with MDA-MB-453. Interestingly, the hydrazide method isolated a number of other N-linked glycoproteins also known to be involved in breast cancer including, epidermal growth factor receptor (EGFR), CD44, and the breast cancer 1, and early onset isoform 1 (BRCA1) biomarker. Analyzing the N-glycoproteins from membranes of breast cancer cell lines highlights the usefulness of the procedure for generating a practical set of potential biomarkers.
doi:10.1021/pr900322g
PMCID: PMC2761014  PMID: 19522481
breast cancer; biomarkers; n-linked glycosylation; glycoprotein; proteomics; mass spectrometry; post-translational modification; hydrazide; HER2; EGFR
7.  Hydrophobic Fractionation Enhances Novel Protein Detection by Mass Spectrometry in Triple Negative Breast Cancer 
It is widely believed that discovery of specific, sensitive and reliable tumor biomarkers can improve the treatment of cancer. The goal of this study was to develop a novel fractionation protocol targeting hydrophobic proteins as possible cancer cell membrane biomarkers. Hydrophobic proteins of breast cancer tissues and cell lines were enriched by polymeric reverse phase columns. The retained proteins were eluted and digested for peptide identification by nano-liquid chromatography with tandem mass spectrometry using a hybrid linear ion-trap Orbitrap.
Hundreds of proteins were identified from each of these three specimens: tumors, normal breast tissue, and breast cancer cell lines. Many of the identified proteins defined key cellular functions. Protein profiles of cancer and normal tissues from the same patient were systematically examined and compared. Stem cell markers were overexpressed in triple negative breast cancer (TNBC) compared with non-TNBC samples. Because breast cancer stem cells are known to be resistant to radiation and chemotherapy, and can be the source of metastasis frequently seen in patients with TNBC, our study may provide evidence of molecules promoting the aggressiveness of TNBC.
The initial results obtained using a combination of hydrophobic fractionation and nano-LC mass spectrometry analysis of these proteins appear promising in the discovery of potential cancer biomarkers. When sufficiently refined, this approach may prove useful for early detection and better treatment of breast cancer.
doi:10.4172/jpb.1000118
PMCID: PMC2894735  PMID: 20596302
Hydrophobic fractionation; Cancer biomarker; Mass spectrometry; Triple negative breast cancer
8.  Accuracy of Clinical Evaluation of Locally Advanced Breast Cancer in Patients Receiving Neoadjuvant Chemotherapy 
Cancer  2009;115(6):1194-1202.
Physical examination (PE), mammography (MG), breast MRI, FDG-PET and pathologic evaluation are used to assess primary breast cancer. Their accuracy has not been well studied in patients receiving neoadjuvant chemotherapy. Accuracies of each modality in tumor and nodal assessment in patients with T3/4 tumors receiving neoadjuvant chemotherapy were compared.
METHODS
45 patients of a prospective clinical trial studying T3-T4M0 tumors were included. Patients received neoadjuvant chemotherapy: docetaxel/carboplatin with or without trastuzumab before and/or after surgery (depending on HER-2/neu status and randomization). Tumor measurements by PE, MG, and MRI and nodal status by PE and PET were obtained before and after neoadjuvant chemotherapy. Concordance among different clinical measurements was assessed and compared with the tumor and nodal staging by pathology. Spearman corr (r) and root mean square error (RMSE) were used to measure the accuracy of measurements among all modalities and between modalities and pathological tumor size.
RESULTS
Comparing to the tumor size measured by PE, MRI was more accurate than MG at baseline (r 0.559, RMSE 35.4% vs. r 0.046, RMSE 66.1%). After neoadjuvant chemotherapy, PE correlated better with pathology than MG or MRI (r 0.655, RMSE 88.6% vs. r 0.146, RMSE 147.1% and r 0.364, RMSE 92.6%). Axillary nodal assessment after neoadjuvant chemotherapy showed high specificity but low sensitivity by PET and PE.
CONCLUSION
Findings suggested that MRI was a more accurate imaging study at baseline for T3/T4 tumor and PE correlated best with pathology finding. PET and PE both correctly predicted positive axillary nodes but not negative nodes.
doi:10.1002/cncr.24154
PMCID: PMC2761029  PMID: 19156919
9.  Proteomics and Mass Spectrometry for Cancer Biomarker Discovery 
Biomarker Insights  2007;2:347-360.
Proteomics is a rapidly advancing field not only in the field of biology but also in translational cancer research. In recent years, mass spectrometry and associated technologies have been explored to identify proteins or a set of proteins specific to a given disease, for the purpose of disease detection and diagnosis. Such biomarkers are being investigated in samples including cells, tissues, serum/plasma, and other types of body fluids. When sufficiently refined, proteomic technologies may pave the way for early detection of cancer or individualized therapy for cancer. Mass spectrometry approaches coupled with bioinformatic tools are being developed for biomarker discovery and validation. Understanding basic concepts and application of such technology by investigators in the field may accelerate the clinical application of protein biomarkers in disease management.
PMCID: PMC2717808  PMID: 19662217
Proteomics; Mass spectrometry; Cancer; Biomarkers

Results 1-9 (9)