The proteomic profiles from two distinct ovarian endometrioid tumor derived cell lines, (MDAH-2774 and TOV-112D) each with different morphological characteristics and genetic mutations, have been studied. Characterization of the differential global protein expression between these two cell lines has important implications for the understanding of the pathogenesis of ovarian endometrioid carcinoma. In this comparative proteomic study, extensive fractionation of peptides generated from whole cell trypsin digestion was achieved by coupling capillary isoelectric focusing (cIEF) in the first dimensional separation with capillary liquid chromatography (RP-HPLC) in the second dimensional separation. On-line analysis was performed using tandem mass spectra acquired by a linear ion trap mass spectrometer from triplicate runs. A total of 1749 and 1955 proteins with protein probability above 0.95 were identified from MDAH-2774 and TOV-112D after filtering through Peptide Prophet/ Protein Prophet software. Differentially expressed proteins were further investigated by Ingenuity Pathway Analysis (IPA) to reveal the association with important biological functions. Canonical pathway analysis using IPA demonstrates that important signaling pathways are highly associated with one of these two cell lines versus the other, such as the PI3K/AKT pathway which is found to be significantly predominant in MDAH-2774 but not in TOV-112D. Also, protein network analysis using IPA highlights p53 as a central hub relating to other proteins from the connectivity map. These results illustrate the utility of high throughput proteomics methods using large scale proteome profiling combined with bioinformatics tools to identify differential signaling pathways, thus contributing to the understanding of mechanisms of deregulation in neoplastic cells.

Analyzing subpopulations of tumor cells in tissue is a challenging subject in proteomic studies. Pancreatic cancer stem cells (CSCs) are such a group of cells that only constitute 0.2-0.8% of the total tumor cells but have been found to be the origin of pancreatic cancer carcinogenesis and metastasis. Global proteome profiling of pancreatic CSCs from xenograft tumors in mice is a promising way to unveil the molecular machinery underlying the signaling pathways. However, the extremely low availability of pancreatic tissue CSCs (around 10,000 cells per xenograft tumor or patient sample) has limited the utilization of currently standard proteomic approaches which do not work effectively with such a small amount of material. Herein, we describe the profiling of the proteome of pancreatic CSCs using a capillary scale shotgun technique by coupling offline capillary isoelectric focusing(cIEF) with nano reversed phase liquid chromatography(RPLC) followed by spectral counting peptide quantification. A whole cell lysate from 10,000 cells which corresponds to ∼1ug protein material is equally divided for three repeated cIEF separations where around 300ng peptide material is used in each run. In comparison with a non-tumorigenic tumor cell sample, among 1159 distinct proteins identified with FDR less than 0.2%, 169 differentially expressed proteins are identified after multiple testing corrections where 24% of the proteins are upregulated in the CSCs group. Ingenuity Pathway analysis of these differential expression signatures further suggests significant involvement of signaling pathways related to apoptosis, cell proliferation, inflammation and metastasis.

We have recently demonstrated that Notch pathway blockade by γ-secretase inhibitor (GSI) depletes cancer stem cells (CSCs) in Glioblastoma Multiforme (GBM) through reduced proliferation and induced apoptosis. However, the detailed mechanism by which the manipulation of Notch signal induces alterations on post-translational modifications such as glycosylation has not been investigated. Herein, we present a differential profiling work to detect the change of glycosylation pattern upon drug treatment in GBM CSCs. Rapid screening of differential cell surface glycan structures has been performed by lectin microarray on live cells followed by the detection of N-linked glycoproteins from cell lysates using multi-lectin chromatography and label-free quantitative mass spectrometry analysis. A total of 51 and 52 glycoproteins were identified in the CSC- and GSI-treated groups, respectively, filtered by a combination of decoy database searching and Trans-Proteomic Pipeline (TPP) processing. Although no significant changes were detected from the lectin microarray experiment, 7 differentially expressed glycoproteins with high confidence were captured after the multi-lectin column including key enzymes involved in glycan processing. Functional annotations of the altered glycoproteins suggest a phenotype transformation of CSCs toward a less tumorigenic form upon GSI treatment.

The characterization of conjugation sites in bioconjugates is critical in the early discovery phase because site-specific conjugation improves in vivo stability and drug efficacy. We previously developed an engineered monoclonal antibody (mAb) scaffold which enables site-specific conjugation toward a reactive lysine (Lys) residue on each heavy chain (HC) by using an azetidinone (AZD) linker. In order to explore conjugations in other location which avoids potential interference with target binding, other chemical linkers have been studied and the investigation of N-hydroxysuccinimade (NHS) linker is reported here. The complexity of identifying the sites lies in part to the large number of Lys residues available for conjugation on the mAb scaffold. This has posed technical challenges to standard peptide mapping approaches. Therefore, an alternative strategy intended for a rapid analysis has been investigated by coupling immuno-affinity capture to matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). In this study, we have employed a novel application of two different capture formats: Surface enhanced laser dissociation/ionization (SELDI) and mass spectrometry immunoassay (MSIA) tips to reduce the analysis time. An antibody against the pharmacophore portion was immobilized to capture the conjugated peptides, and subsequently provide characterization of the conjugation sites on the scaffold. Multiple sites for the AZD and NHS linkers have been easily identified and confirmed by MS2 sequencing. Lysine99 is the predominant site for the AZD linker, and Lysine55 is the primary site for the NHS linker with Lysine193 and Tyrosine37 being minor sites as shown in the abstract figure. We have also demonstrated the use of conjugation mapping to compare the distribution pattern between the AZD and NHS linkers as well as to study the stability of conjugation sites in a rapid way.

Notch Signaling has been demonstrated to have a central role in Glioblastoma (GBM) Cancer Stem Cells (CSCs) and we have demonstrated recently that Notch pathway blockade by γ-secretase inhibitor (GSI) depletes GBM CSCs and prevents tumor propagation both in vitro and in vivo. In order to understand the proteome alterations involved in this transformation, a dose-dependent quantitative mass spectrometry (MS) based proteomic study has been performed based on global proteome profiling and a target verification phase where both Immunoassay and a Multiple Reaction Monitoring (MRM) assay are employed. The selection of putative protein candidates for confirmation poses a challenge due to the large number of identifications from the discovery phase. A multilevel filtering strategy together with literature mining is adopted to transmit the most confident candidates along the pipeline. Our results indicate that treating GBM CSCs with GSI induces a phenotype transformation towards non-tumorigenic cells with decreased proliferation and increased differentiation, as well as elevated apoptosis. Suppressed glucose metabolism and attenuated NFR2-mediated oxidative stress response are also suggested from our data, possibly due to their crosstalk with Notch Signaling. Overall, this quantitative proteomic based dose-dependent work complements our current understanding of the altered signaling events occurring upon the treatment of GSI in GBM CSCs.