The Surfaceome: Methods and Protocols

ISBN-13: 9781493985180 / Angielski / Miękka / 2018 / 348 str.

Kenneth R. Boheler; Rebekah L. Gundry

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Discovery-Based Approaches to Surfaceome Content

1. Surfaceome Analysis Protocol for the Identification of Novel Bordetella pertussis Antigens

Yulanda M. Williamson, Jennifer Whitmon, Rolieria West-Deadwyler, Hercules Moura, Adrian R. Woolfitt, Jon Rees, David Schieltz, and John R. Barr

2. “Shaving” Live Bacterial Cells with Proteases for Proteomic Analysis of Surface Proteins

Manuel J. Rodríguez-Ortega

3. Methods for Mapping the Extracellular and Membrane Proteome in the Avian Embryo, and Identification of Putative Vascular Targets or Endothelial Genes

Witold W. Kilarski, John Herbert, and Andreas Bikfalvi 

4. Mass Spectrometry Based Identification of Extracellular Domains of Cell Surface N-Glycoproteins: Defining the Accessible Surfaceome for Immunophenotyping Stem Cells and their Derivatives

Chelsea M. Fujinaka, Matthew Waas, and Rebekah L. Gundry

5. Application of Higher Density Iron Oxide Nanoparticle Pellicles to Enrich the Plasma Membrane and its Proteome from Cells in Suspension

Rebecca L. Rose, Waeowalee Choksawangkarn, and Catherine Fenselau

6. Proteomic Profiling of Secreted Proteins, Exosomes, and Microvesicles in Cell Culture Conditioned Media

Ankit Sinha, Simona Principe, Javier Alfaro, Alex Ignatchenko, Vladimir Ignatchenko, and Thomas Kislinger

Part II Targeted Approaches for Surfaceome Content

7. Cloning, Expression, and Purification of the Glycosylated Transmembrane Protein, Cation-Dependent Mannose 6-phosphate Receptor, from Sf9 Cells Using the Baculovirus System

Linda J. Olson and Nancy M. Dahms

8. Bispecific Antibody Armed T Cells to Target Cancer Cells

Archana Thakur, Lawrence G. Lum, and Sandeep Mittal

9. Immunophenotyping of Live Human Pluripotent Stem Cells by Flow Cytometry

Daniel R. Riordon and Kenneth R. Boheler

10. Detecting Cell Surface Expression of the G Protein-Coupled Receptor CXCR4 Amanda M. Nevins and Adriano Marchese

Part III Cell-Based Functional Analyses Related to Surfaceome Content 

11. NaV Channels: Assaying Biosynthesis, Trafficking, Function

Gordon F. Tomaselli and Federica Farinelli

12. High-Content Electrophysiological Analysis of Human Pluripotent Stem Cell-Derived Cardiomyocytes (hPSC-CMs)

Chi-Wing Kong, Lin Geng, and Ronald A. Li

13. Methods for Evaluation of Vascular Endothelial Cell Function with Transient Receptor Potential (TRP) Channel Drugs

Yung Wui Tjong and Xiaoqiang Yao

14. Methods to Study the Signal Transduction of the Surface Receptor Tyrosine Kinase TrkB in Neurons

Kwok-On Lai and Nancy Y. Ip

15. Polarized Human Retinal Pigment Epithelium Exhibits Distinct Surface Proteome on Apical and Basal Plasma Membranes

Vladimir Khristov, Qin Wan, Ruchi Sharma, Mostafa Lotfi, Arvydas Maminishkis, and Kapil Bharti

16. Extracellular Matrix Molecule-Based Capture of Mesenchymal Stromal Cells under Flow

Teresa Massam-Wu, Stuart A. Cain, and Catherine M. Kielty

17. Generation of Induced Pluripotent Stem Cells from Patients with COL3A1 Mutations and Differentiation to Smooth Muscle Cells for ECM-Surfaceome Analyses 

Jiaozi He, Zhihui Weng, Stanley Chun Ming Wu, and Kenneth R. Boheler

18. Fabrication and Mechanical Properties Measurements of 3D Microtissues for the Study of Cell-Matrix Interactions

Prasenjit Bose, Chen Yu Huang, Jeroen Eyckmans, Christopher S. Chen, and Daniel H. Reich

Part IV Computational Approaches in Surfaceome Studies

19. Discovery of Surface Target Proteins Linking Drugs, Molecular Markers, Gene Regulation, Protein Networks, and Disease by Using a Web-Based Platform Targets-Search

Bin Yan, Pangwen Wang, Junwen Wang, and Kenneth R. Boheler

Blurb

This volume provides readers with the latest techniques and tools to assess modifications and functions of the surfaceome. The chapters in this book are divided into 4 sections: discovery-based approaches to surfaceome content; targeted approaches for surfaceome content; cell-based function analyses related to surfaceome content; and computational approaches in surfaceome studies. Section 1 focuses on discovery-based approaches for cataloging surfaceome content that analyses the surfaceome of bacteria, avian embryos, and mammalian systems. Section 2 discusses methods that over-express specific targets in Sf9 cells and generate bi-specific antibodies for targeting cancer and somatic cells. Section 3 explores voltage dependent sodium channels and high-content electrophysiological analyses. The final section looks at the new web-based platform known as targets-search. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Comprehensive and thorough, Surfaceome: Methods and Protocols assists in the study of cell surface protein biology and function. It is a valuable resource for all researchers interested in this field.