Identification of Altered Cell Surface Glycoproteins and Micropattern Assay Development in the Context of Human Malignancies


Book Description

Metastatic melanoma and relapsed acute T cell lymphoblastic leukemia remain incurable despite major advancements in our understanding of these cancers. In some ways, the foundation for a cure has already been laid; many molecular targets for drug development are now clearly defined, and recently novel therapeutics have shown promise in the clinical setting. However, this immense progress has not translated into a marked increase in patient survival. This graduate project focused on two aims, which with further research and development may lead to a cure for these cancers. First, the development of a cellular-based high-throughput synergistic assay was looked at, that would allow for rapid screening of multiple drug combinations. Second, cancer-specific alterations in the cell surface high mannose glycoprotein profile were identified in the context of metastatic melanoma and T-ALL cells. The feasibility of these two aims is demonstrated by existing innovations and research. First, protein microarrays have been developed to isolate and characterize a variety of cell types. Second, growth factors and other molecules have been successfully printed onto these arrays. Third, cancer cells and cancer stem cells have been previously shown to have alterations in their cell surface glycome. As part of the first project, micropatterned silane and polyethylene glycol (PEG) coated glass slides were successfully developed, with these modifications acting as a non-fouling surface for cell attachment. On these slides cell-specific antibodies, antiCD3 and anti-GD3, were printed and demonstrated successful capture ofT-ALL and melanoma cell lines, respectively. However, the effectiveness of this cell capture needs further improvement, with regards to uniform cell seeding. Future studies will utilize recently developed epoxide coated slides, which allow for covalent attachment of capture antibodies. Additionally, anti-CD4 antibody will be printed for T-ALL cell capture. With respect to the characterization of the cell surface glycome of malignant melanoma and TALL cell lines versus their non- or less-malignant counterparts, we were able to successfully demonstrate that MHC class I and sodium/potassium A TPase proteins were differentially glycosylated on both of these diverging cancers. MHC class I had significantly higher expression on high metastatic potential B 16F 10 cells compared to B16FO cells (p-value = 0.014), and in Jurkat cells as compared to normal pan T cells (pvalue = 0.011). Additionally, sodium/potassium ATPase had significantly higher expression on B16F10 (p-value = 0.028) and Jurkat cells (p-value = 0.013) verses B16F0 and normal T cells, respectively. These proteins, along with other identified high mannose surface proteins are directly linked to cancer cell proliferation promotion. Additionally, the altered glycosylation patterns identified in this graduate project may have a direct impact on MHC class I and sodium/potassium A TPase' s roles in cancer cell promotion. Based on obtained data, future studies will focus on conforming the presence of identified proteins on the cell surface through antigen immunofluorescence labeling, and foot printing of high mannose glycans. Footprinting will be done to both determine the extent of glycosylation modifications occurring on cancer cells, as well to characterize any changes in protein conformation due to changes in glycosylation, as determined through in silica modeling.




Chemical Glycoproteomics for Identification and Discovery of Glycoprotein Alterations in Human Cancer


Book Description

Changes in glycosylation have long been appreciated to be part of the cancer phenotype; sialylated glycans are found at elevated levels on many types of cancer and have been implicated in disease progression. However, the specific glycoproteins that contribute to cell surface sialylation are not well characterized, specifically in bona fide human cancer. Metabolic and bioorthogonal labeling methods have previously enabled enrichment and identification of sialoglycoproteins from cultured cells and model organisms. The goal of this work was to develop technologies that can be used for detecting changes in glycoproteins in clinical models of human cancer. In Chapter 1 of this dissertation, I present an overview of the structures and functions of glycans and their relationship to cancer progression. I also discuss applications of in vivo bioorthogonal labeling in model organisms and how in humans, the significant regulatory and ethical barriers associated with introducing chemically altered sugars into people have hindered it. Finally, I review mass spectrometry-based proteomics and how it can be applied to clinical glycoproteomics. In Chapter 2, I demonstrate the first application of this bioorthogonal labeling in a glycoproteomics platform applied to human tissues cultured ex vivo. Both normal and cancerous prostate tissues were sliced and cultured in the presence of functionalized derivatives of N-acetyl mannosamine, the sialic acid biosynthetic precursor. Chemical biotinylation followed by enrichment and mass spectrometry led to the identification of glycoproteins that were found at elevated levels or uniquely in cancerous prostate tissue. This work therefore extends the use of bioorthogonal labeling strategies to problems of human clinical relevance. Secretome proteins play important roles in regulation of many physiological processes and show utility as potential biomarkers and for noninvasive diagnostics and treatment monitoring. In Chapter 3, I discuss a platform for identifying sialoglycoproteins that were secreted in the conditioned media from bioorthogonally labeled human prostate tissue slice cultures. This platform could be used to identify disease biomarkers in a faithful clinical model of human disease. Mutations in granulocyte colony-stimulating factor 3 receptor (CSF3R), also known as G-CSFR, occur in the majority of patients with chronic neutrophilic leukemia (CNL) and are more rarely present in other kinds of leukemia. In Chapter 4, I discuss novel variants in CSF3R at asparagine residue N610, one of which was germline. Interestingly, these N610 substitutions are potently oncogenic and result in ligand-independent receptor activation. They confer activation of the JAK-STAT signaling pathway and concurrent sensitivity to JAK kinase inhibitors. The N610 residue is part of a consensus N-linked glycosylation motif in the receptor. Detailed mass spectrometry analysis demonstrates that this site is occupied by both complex and complex bisecting glycans. Further analysis demonstrates that N610 is the primary site of sialylation of the receptor. This study demonstrates that membrane-proximal N-linked glycosylation is critical for maintaining the ligand dependence of the receptor. Furthermore, it expands the repertoire of potently oncogenic mutations in CSF3R that are therapeutically targetable.




Tumor Organoids


Book Description

Cancer cell biology research in general, and anti-cancer drug development specifically, still relies on standard cell culture techniques that place the cells in an unnatural environment. As a consequence, growing tumor cells in plastic dishes places a selective pressure that substantially alters their original molecular and phenotypic properties.The emerging field of regenerative medicine has developed bioengineered tissue platforms that can better mimic the structure and cellular heterogeneity of in vivo tissue, and are suitable for tumor bioengineering research. Microengineering technologies have resulted in advanced methods for creating and culturing 3-D human tissue. By encapsulating the respective cell type or combining several cell types to form tissues, these model organs can be viable for longer periods of time and are cultured to develop functional properties similar to native tissues. This approach recapitulates the dynamic role of cell–cell, cell–ECM, and mechanical interactions inside the tumor. Further incorporation of cells representative of the tumor stroma, such as endothelial cells (EC) and tumor fibroblasts, can mimic the in vivo tumor microenvironment. Collectively, bioengineered tumors create an important resource for the in vitro study of tumor growth in 3D including tumor biomechanics and the effects of anti-cancer drugs on 3D tumor tissue. These technologies have the potential to overcome current limitations to genetic and histological tumor classification and development of personalized therapies.




The Physics of Cancer


Book Description

Recent years have witnessed an increasing number of theoretical and experimental contributions to cancer research from different fields of physics, from biomechanics and soft-condensed matter physics to the statistical mechanics of complex systems. Reviewing these contributions and providing a sophisticated overview of the topic, this is the first book devoted to the emerging interdisciplinary field of cancer physics. Systematically integrating approaches from physics and biology, it includes topics such as cancer initiation and progression, metastasis, angiogenesis, cancer stem cells, tumor immunology, cancer cell mechanics and migration. Biological hallmarks of cancer are presented in an intuitive yet comprehensive way, providing graduate-level students and researchers in physics with a thorough introduction to this important subject. The impact of the physical mechanisms of cancer are explained through analytical and computational models, making this an essential reference for cancer biologists interested in cutting-edge quantitative tools and approaches coming from physics.




Physics of Cancer


Book Description

This revised second edition is improved linguistically with multiple increases of the number of figures and the inclusion of several novel chapters such as actin filaments during matrix invasion, microtubuli during migration and matrix invasion, nuclear deformability during migration and matrix invasion, and the active role of the tumor stroma in regulating cell invasion.




Industrial Pharmaceutical Biotechnology


Book Description

This volume focuses on pharmaceutical biotechnology as a key area of life sciences. The complete range of concepts, processes and technologies of biotechnology is applied in modern industrial pharmaceutical research, development and production. The results of genome sequencing and studies of biological-genetic function are combined with chemical, micro-electronic and microsystem technology to produce medical devices and diagnostic biochips. A multitude of biologically active molecules is expanded by additional novel structures created with newly arranged gene clusters and bio-catalytic chemical processes. New organisational structures in the co-operation of institutes, companies and networks enable faster knowledge and product development and immediate application of the results of research and process development. This book is the ideal source of information for scientists and engineers in research and development, for decision-makers in biotech, pharma and chemical corporations, as well as for research institutes, but also for founders of biotech companies and people working for venture capital corporations.




Biosensors for Virus Detection


Book Description

Developments and applications of biosensor platforms for analysis of viral infections including Coronavirus, HIV, Hepatitis, Ebola, Zika, Norovirus, Influenza, SARS etc. Embraces properties, fabrication, and recent research regarding optical, electrochemical, piezoelectric, fluorescence, thermal, magnetic and micromechanical sensor families.







Electrospun Nanofibers


Book Description

Electrospun Nanofibers covers advances in the electrospinning process including characterization, testing and modeling of electrospun nanofibers, and electrospinning for particular fiber types and applications. Electrospun Nanofibers offers systematic and comprehensive coverage for academic researchers, industry professionals, and postgraduate students working in the field of fiber science. Electrospinning is the most commercially successful process for the production of nanofibers and rising demand is driving research and development in this field. Rapid progress is being made both in terms of the electrospinning process and in the production of nanofibers with superior chemical and physical properties. Electrospinning is becoming more efficient and more specialized in order to produce particular fiber types such as bicomponent and composite fibers, patterned and 3D nanofibers, carbon nanofibers and nanotubes, and nanofibers derived from chitosan. Provides systematic and comprehensive coverage of the manufacture, properties, and applications of nanofibers Covers recent developments in nanofibers materials including electrospinning of bicomponent, chitosan, carbon, and conductive fibers Brings together expertise from academia and industry to provide comprehensive, up-to-date information on nanofiber research and development Offers systematic and comprehensive coverage for academic researchers, industry professionals, and postgraduate students working in the field of fiber science




Structural Immunology


Book Description

This book presents a comprehensive overview of important immune molecules and their structure-function relationships. The immune system is highly complex, consisting of a network of molecules, cells, tissues and organs, and the immune reaction is involved in various physiological as well as pathological processes, including development, self-tolerance, infection, immunity, and cancer. Numerous molecules participate in immune recognition, inhibition and activation, and these important immune molecules can be roughly divided into cell surface receptors, intracellular receptors and intracellular signaling molecules. The study of how these immune molecules function at molecular level has laid the foundation for understanding the immune system. The book provides researchers and students with the latest research advances concerning the structural biology of key immune molecules/pathways, and offers immunologists essential insights into how these immune molecules function.