Karen L. Abbott

Identification of candidate biomarkers with cancer-specific glycosylation in the tissue and serum of endometrioid ovarian cancer patients by glycoproteomic analysis.

Epithelial ovarian cancer is diagnosed less than 25% of the time when the cancer is confined to the ovary, leading to 5‐year survival rates of less than 30%. Therefore, there is an urgent need for early diagnostics for ovarian cancer. Our study using glycotranscriptome comparative analysis of endometrioid ovarian cancer tissue and normal ovarian tissue led to the identification of distinct differences in the transcripts of a restricted set of glycosyltransferases involved in N‐linked glycosylation. Utilizing lectins that bind to glycan structures predicted to show changes, we observed differences in lectin‐bound glycoproteins consistent with some of the transcript differences. In this study, we have extended our observations by the use of selected lectins to perform a targeted glycoproteomic analysis of ovarian cancer and normal ovarian tissues. Our results have identified several glycoproteins that display tumor‐specific glycosylation changes. We have verified these glycosylation changes on glycoproteins from tissue using immunoprecipitation followed by lectin blot detection. The glycoproteins that were verified were then analyzed further using existing microarray data obtained from benign ovarian adenomas, borderline ovarian adenocarcinomas, and malignant ovarian adenocarcinomas. The verified glycoproteins found to be expressed above control levels in the microarray data sets were then screened for tumor‐specific glycan modifications in serum from ovarian cancer patients. Results obtained from two of these glycoprotein markers, periostin and thrombospondin, have confirmed that tumor‐specific glycan changes can be used to distinguish ovarian cancer patient serum from normal serum.

Targeted Glycoproteomic Identification of Biomarkers for Human Breast Carcinoma

Glycosylation is a dynamic post-translational modification that changes during the development and progression of various malignancies. During the oncogenesis of breast carcinoma, the glycosyltransferase known as N-acetylglucosaminyltransferase Va (GnT-Va) transcript levels and activity are increased due to activated oncogenic signaling pathways. Elevated GnT-V levels leads to increased beta(1,6)-branched N-linked glycan structures on glycoproteins that can be measured using a specific carbohydrate binding protein or lectin known as L-PHA. L-PHA does not bind to nondiseased breast epithelial cells, but during the progression to invasive carcinoma, cells show a progressive increase in L-PHA binding. We have developed a procedure for intact protein L-PHA-affinity enrichment, followed by nanospray ionization mass spectrometry (NSI-MS/MS), to identify potential biomarkers for breast carcinoma. We identified L-PHA reactive glycoproteins from matched normal (nondiseased) and malignant tissue isolated from patients with invasive ductal breast carcinoma. Comparison analysis of the data identified 34 proteins that were enriched by L-PHA fractionation in tumor relative to normal tissue for at least 2 cases of ductal invasive breast carcinoma. Of these 34 L-PHA tumor enriched proteins, 12 are common to all 4 matched cases analyzed. These results indicate that lectin enrichment strategies targeting a particular glycan change associated with malignancy can be an effective method of identifying potential biomarkers for breast carcinoma.

Focused glycomic analysis of the N-linked glycan biosynthetic pathway in ovarian cancer

Epithelial ovarian cancer is the deadliest female reproductive tract malignancy in Western countries. Less than 25% of cases are diagnosed when the cancer is confined, however, pointing to the critical need for early diagnostics for ovarian cancer. Identifying the changes that occur in the glycome of ovarian cancer cells may provide an avenue to develop a new generation of potential biomarkers for early detection of this disease. We performed a glycotranscriptomic analysis of endometrioid ovarian carcinoma using human tissue, as well as a newly developed mouse model that mimics this disease. Our results show that the N‐linked glycans expressed in both nondiseased mouse and human ovarian tissues are similar; moreover, malignant changes in the expression of N‐linked glycans in both mouse and human endometrioid ovarian carcinoma are qualitatively similar. Lectin reactivity was used as a means for rapid validation of glycan structural changes in the carcinomas that were predicted by the glycotranscriptome analysis. Among several changes in glycan expression noted, the increase of bisected N‐linked glycans and the transcripts of the enzyme responsible for its biosynthesis, GnT‐III, was the most significant. This study provides evidence that glycotranscriptome analysis can be an important tool in identifying potential cancer biomarkers.

Receptor Tyrosine Phosphatase β (RPTPβ) Activity and Signaling Are Attenuated by Glycosylation and Subsequent Cell Surface Galectin-1 Binding

O-Mannosyl-linked glycosylation is abundant within the central nervous system, yet very few glycoproteins with this glycan modification have been identified. Congenital diseases with significant neurological defects arise from inactivating mutations found within the glycosyltransferases that act early in the O-mannosyl glycosylation pathway. The N-acetylglucosaminyltransferase known as GnT-Vb or -IX is highly expressed in brain and branches O-mannosyl-linked glycans. Our results using SH-SY5Y neuroblastoma cells indicate that GnT-Vb activity promotes the addition of the O-mannosyl-linked HNK-1 modification found on the developmentally regulated and neuron-specific receptor protein-tyrosine phosphatase β (RPTPβ). These changes in glycosylation accompany decreased cell-cell adhesion and increased rates of migration on laminin. In addition, we show that expression of GnT-Vb promotes its dimerization and inhibits RPTPβ intrinsic phosphatase activity, resulting in higher levels of phosphorylated β-catenin, suggesting a mechanism by which GnT-Vb glycosylation couples to changes in cell adhesion. GnT-Vb-mediated glycosylation of RPTPβ promotes galectin-1 binding and RPTPβ levels of retention on the cell surface. N-Acetyllactosamine, but not sucrose, treatment of cells results in decreased RPTP retention, showing that galectin-1 binding contributes to the increased retention after GnT-Vb expression. These results place GnT-Vb as a regulator of RPTPβ signaling that influences cell-cell and cell-matrix interactions in the developing nervous system.

NMR structure of a complex containing the TFIIF subunit RAP74 and the RNA polymerase II carboxyl-terminal domain phosphatase FCP1

FCP1 [transcription factor IIF (TFIIF)-associated carboxyl-terminal domain (CTD) phosphatase] is the only identified phosphatase specific for the phosphorylated CTD of RNA polymerase II (RNAP II). The phosphatase activity of FCP1 is enhanced in the presence of the large subunit of TFIIF (RAP74 in humans). It has been demonstrated that the CTD of RAP74 (cterRAP74; residues 436–517) directly interacts with the highly acidic CTD of FCP1 (cterFCP; residues 879–961 in human). In this manuscript, we have determined a high-resolution solution structure of a cterRAP74/cterFCP complex by NMR spectroscopy. Interestingly, the cterFCP protein is completely disordered in the unbound state, but forms an α-helix (H1′; E945–M961) in the complex. The cterRAP74/cterFCP binding interface relies extensively on van der Waals contacts between hydrophobic residues from the H2 and H3 helices of cterRAP74 and hydrophobic residues from the H1′ helix of cterFCP. The binding interface also contains two critical electrostatic interactions involving aspartic acid residues from H1′ of cterFCP and lysine residues from both H2 and H3 of cterRAP74. There are also three additional polar interactions involving highly conserved acidic residues from the H1′ helix. The cterRAP74/cterFCP complex is the first high-resolution structure between an acidic residue-rich domain from a holoenzyme-associated regulatory protein and a general transcription factor. The structure defines a clear role for both hydrophobic and acidic residues in protein/protein complexes involving acidic residue-rich domains in transcription regulatory proteins.

Lectin-based glycoproteomic techniques for the enrichment and identification of potential biomarkers.

Glycan structures on glycoproteins are controlled by several factors such as regulated expression of glycosyltransferases and glycosylhydrolases, as well as regulation of glycoprotein expression, folding, and transport through the ER and Golgi. In cancer, for example, the glycosylation of glycoproteins can be significantly altered due to changes in the expression levels of glycosyltransferases as a result of oncogene activated signaling pathways coupled with gain or loss in chromosome copy number. Cumulatively these changes result in glycoproteins exported to the cell surface and extracellular region with altered glycan structures that can lead to significant changes in cell phenotype. Therefore, it is advantageous to be able to capture and identify proteins that express particular glycans or classes of glycans. In this report, we discuss extraction methods and lectin capture methodology that can be used to enrich and identify by mass spectrometry glycoproteins that express specific glycans that change in response to disorders or diseases, such as the presence of malignancies.

Three-Year Outcome of the Halt Trial: A Prospective Analysis of Radiofrequency Volumetric Thermal Ablation of Myomas

STUDY OBJECTIVE To analyze the clinical success of radiofrequency volumetric thermal ablation (RFVTA) at 3-year follow-up in terms of subject responses to validated questionnaires and surgical repeat intervention to treat myomas. DESIGN Prospective follow-up of patients for 36 months after treatment in a multicenter international trial of outpatient, laparoscopic ultrasound-guided RFVTA of symptomatic uterine myomas (Canadian Task Force classification II-1). SETTING University hospitals and private surgical centers. PATIENTS One hundred thirty-five premenopausal women (mean [SD] age, 42.5 [4.6] years; body mass index, 30.5 [6.1]) with symptomatic uterine myomas and objectively confirmed heavy menstrual bleeding (≥ 160 to ≤ 500 mL). INTERVENTIONS Laparoscopic ultrasound-guided RFVTA. MEASUREMENTS AND MAIN RESULTS One hundred four participants were followed prospectively for 36 months after treatment of myomas via RFVTA. For 104 evaluable participants with 36-month data, change in mean (SD) symptom severity from baseline (60.2 [18.8]) to 36 months was -32.6 (95% confidence interval, -37.5 to -27.8; p < .001). Health-related quality of life also was improved, from the baseline value of 39.2 (19.2) to 38.6 (95% confidence interval, 33.3 to 43.9; p < .001) at 36 months. Patient-reported Uterine Fibroid Symptom and Health-Related Quality of Life questionnaire subscores demonstrated statistically significant improvement from baseline to 36 months in all categories (Concern, Activities, Energy/Mood, Control, Self-consciousness, and Sexual Function) (p < .001). For the 104 participants with 36-month data, mean state of health scores (EuroQOL-5D Health State Index) improved from a baseline value of 71.0 (19.3) to 86.2 (11.7) at 36 months. The cumulative repeat intervention rate of 11% (14 of 135 participants) at 36 months was well below the possible 25% maximum expected at the beginning of the trial. CONCLUSION RFVTA of uterine myomas resulted in sustained relief from myoma symptoms and continued improvement in health-related quality of life through 36 months after ablation. The low repeat intervention data through 36 months is a positive outcome for patient well-being.

Proteomic identification of glycosylphosphatidylinositol anchor-dependent membrane proteins elevated in breast carcinoma

Background: GPI-anchored proteins are elevated in breast carcinoma. Results: We utilized mass spectrometry and molecular biology techniques to capture and identify GPI-anchored proteins from breast carcinoma. Conclusion: Increased levels of GPI anchor addition contributes to the dedifferentiation of malignant breast epithelial cells. Significance: We have identified new potential diagnostic and therapeutic targets for breast carcinoma. The glycosylphosphatidylinositol (GPI) anchor is a lipid and glycan modification added to the C terminus of certain proteins in the endoplasmic reticulum by the activity of a multiple subunit enzyme complex known as the GPI transamidase (GPIT). Several subunits of GPIT have increased expression levels in breast carcinoma. In an effort to identify GPI-anchored proteins and understand the possible role of these proteins in breast cancer progression, we employed a combination of strategies. First, alpha toxin from Clostridium septicum was used to capture GPI-anchored proteins from human breast cancer tissues, cells, and serum for proteomic analysis. We also expressed short interfering RNAs targeting the expression of the GPAA1 and PIGT subunits of GPIT in breast cancer cell lines to identify proteins in which membrane localization is dependent on GPI anchor addition. Comparative membrane proteomics using nano-ESI-RPLC-MS/MS led to the discovery of several new potential diagnostic and therapeutic targets for breast cancer. Furthermore, we provide evidence that increased levels of GPI anchor addition in malignant breast epithelial cells promotes the dedifferentiation of malignant breast epithelial cells in part by increasing the levels of cell surface markers associated with mesenchymal stem cells.

Mannose receptor (MR) engagement by mesothelin GPI anchor polarizes tumor-associated macrophages and is blocked by anti-MR human recombinant antibody.

Tumor-infiltrating macrophages respond to microenvironmental signals by developing a tumor-associated phenotype characterized by high expression of mannose receptor (MR, CD206). Antibody cross-linking of CD206 triggers anergy in dendritic cells and CD206 engagement by tumoral mucins activates an immune suppressive phenotype in tumor-associated macrophages (TAMs). Many tumor antigens are heavily glycosylated, such as tumoral mucins, and/or attached to tumor cells by mannose residue-containing glycolipids (GPI anchors), as for example mesothelin and the family of carcinoembryonic antigen (CEA). However, the binding to mannose receptor of soluble tumor antigen GPI anchors via mannose residues has not been systematically studied. To address this question, we analyzed the binding of tumor-released mesothelin to ascites-infiltrating macrophages from ovarian cancer patients. We also modeled functional interactions between macrophages and soluble mesothelin using an in vitro system of co-culture in transwells of healthy donor macrophages with human ovarian cancer cell lines. We found that soluble mesothelin bound to human macrophages and that the binding depended on the presence of GPI anchor and of mannose receptor. We next challenged the system with antibodies directed against the mannose receptor domain 4 (CDR4-MR). We isolated three novel anti-CDR4-MR human recombinant antibodies (scFv) using a yeast-display library of human scFv. Anti-CDR4-MR scFv #G11 could block mesothelin binding to macrophages and prevent tumor-induced phenotype polarization of CD206low macrophages towards TAMs. Our findings indicate that tumor-released mesothelin is linked to GPI anchor, engages macrophage mannose receptor, and contributes to macrophage polarization towards TAMs. We propose that compounds able to block tumor antigen GPI anchor/CD206 interactions, such as our novel anti-CRD4-MR scFv, could prevent tumor-induced TAM polarization and have therapeutic potential against ovarian cancer, through polarization control of tumor-infiltrating innate immune cells.

Non-isotopic in situ hybridization method for mitochondria in oncocytes

We used in situ hybridization to specifically identify mitochondria in a series of formalin-fixed, paraffin-embedded oncocytic lesions. Digoxigenin-labeled DNA probes were generated by the polymerase chain reaction (PCR), with primers designed to amplify a mitochondrion-specific 154 BP sequence within the ND4 coding region. Probes were hybridized with mitochondrial DNA under stringent conditions. Oncocytes were strongly and consistently stained, reflecting the high copy number of mitochondrial DNA within these cells. Because of the presence of endogenous biotin within mitochondria, digoxigenin is preferable to biotin as a label for detection of mitochondria.