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Cancer Systems and Integrative Biology

  • Book
  • © 2023

Overview

Editors:
  1. Usha N. Kasid

    1. Lombardi Comprehensive Cancer Center, Georgetown University, Washington, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Robert Clarke

    1. The Hormel Institute, University of Minnesota, Austin, USA

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2660)

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About this book

This thorough volume explores recent advances that have revolutionized the field of precision oncology. The chapters, contributed by experts in the areas of cancer systems and integrative biology, provide hands-on guidance toward developing tools to monitor spatial and temporal changes in tumors, tracking tumor markers in blood, and ultimately developing precision medicine to combat cancer in real time. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that ensures successful results. 

Authoritative and informative, Cancer Systems and Integrative Biology serves as an invaluable resource for researchers, pharmaceutical scientists, and oncologists interested in expanding their knowledge base in the current developments in cancer research.

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Table of contents (24 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Introduction: Cancer Systems and Integrative Biology

    • Robert Clarke
    Pages 1-11

  3. Genome-Wide Analysis of Palindrome Formation with Next-Generation Sequencing (GAPF-Seq) and a Bioinformatics Pipeline for Assessing De Novo Palindromes in Cancer Genomes

    • Michael M. Murata, Armando E. Giuliano, Hisashi Tanaka
    Pages 13-22

  4. Sample Preparation and Differential Gene Expression Analysis of Human Cancer Cell Lines by RNA Sequencing

    • Dmitry Leshchiner, Tommy V. Vo, Sachi Horibata
    Pages 23-41

  5. Generating Mitochondrial-Nuclear Exchange (MNX) Mice to Identify Mitochondrial Determinants of Cancer Metastasis

    • Danny R. Welch, Melissa A. Larson, Carolyn J. Vivian, Jay L. Vivian
    Pages 43-59

  6. 3D-Autologous Culture Method for Precision Oncology

    • Qian Xu, Meiling Yan, Yao Tang
    Pages 61-68

  7. High-Plex Spatial Profiling of RNA and Protein Using Digital Spatial Profiler

    • Nan Wang, Xia Li, Zhiyong Ding
    Pages 69-83

  8. Integration of Single-Cell RNA-Sequencing and Network Analysis to Investigate Mechanisms of Drug Resistance

    • Stephanie The, Patricia M. Schnepp, Greg Shelley, Jill M. Keller, Arvind Rao, Evan T. Keller
    Pages 85-94

  9. Combination of Tissue Microarray Profiling and Multiplexed IHC Approaches to Investigate Transport Mechanism of Nucleoside Analog Drug Resistance

    • Debasis Nayak, Brenna Weadick, Rajgopal Govindarajan
    Pages 95-121

  10. In Situ Proximity Ligation Assay to Visualize Protein–Protein Interactions in Tumor Specimens

    • Yasuhiro Miki, Erina Iwabuchi, Takashi Suzuki
    Pages 123-135

  11. Integration of Metabolomic and Proteomic Data to Uncover Actionable Metabolic Pathways

    • Christian Heckendorf, Benjamin C. Blum, Weiwei Lin, Matthew L. Lawton, Andrew Emili
    Pages 137-148

  12. Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes

    • April Sagan, Xiaojun Ma, Koushul Ramjattun, Hatice Ulku Osmanbeyoglu
    Pages 149-169

  13. Mass Spectrometry-Based Tissue Imaging of the Tumor Microenvironment

    • Tyler Risom, Patrick Chang, Sandra Rost, James Ziai
    Pages 171-185

  14. Multiplexed Immunoassay Using Quantum Dots to Monitor Proteins Secreted from Single Cells at Near-Single Molecule Resolution

    • Veena Y. Naveen, Tingwei Deng, Vanessa Herrera, Jered B. Haun
    Pages 187-206

  15. Isolation and Identification of Plasma Extracellular Vesicles Protein Biomarkers

    • Michelle V. Lihon, Marco Hadisurya, Xiaofeng Wu, Anton Iliuk, W. Andy Tao
    Pages 207-217

  16. Discovery of a Hidden Proinflammatory Signaling Proteome Using a Large-Scale, Targeted Antibody Microarray Platform

    • Catherine Jozwik, Ofer Eidelman, Meera Srivastava
    Pages 219-233

  17. Multiplex Fluorescent Immunohistochemistry for Preservation of Tumor Microenvironment Architecture and Spatial Relationship of Cells in Tumor Tissues

    • Jake J. McGue, Jacob J. Edwards, Brian D. Griffith, Timothy L. Frankel
    Pages 235-246

  18. Circle Damage Sequencing for Whole-Genome Analysis of DNA Damage

    • Seung-Gi Jin, Jennifer Johnson, Gerd P. Pfeifer
    Pages 247-262

  19. CRISPR-Directed Gene Editing as a Method to Reduce Chemoresistance in Lung Cancer Cells

    • Natalia Rivera-Torres, Pawel Bialk, Eric B. Kmiec
    Pages 263-271

  20. Integrated In Silico Analysis of Proteogenomic and Drug Targets for Pancreatic Cancer Survival

    • Alakesh Bera, Digonto Chatterjee, Jack Hester, Meera Srivastava
    Pages 273-282
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Editors and Affiliations

  • Lombardi Comprehensive Cancer Center, Georgetown University, Washington, USA

    Usha N. Kasid

  • The Hormel Institute, University of Minnesota, Austin, USA

    Robert Clarke

Bibliographic Information

  • Book Title: Cancer Systems and Integrative Biology

  • Editors: Usha N. Kasid, Robert Clarke

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3163-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-3162-1Published: 17 May 2023

  • Softcover ISBN: 978-1-0716-3165-2Due: 17 June 2023

  • eBook ISBN: 978-1-0716-3163-8Published: 16 May 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 375

  • Number of Illustrations: 1 b/w illustrations

  • Topics: Cancer Research, Bioinformatics

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