Biomarkers for immunotherapy of cancer : methods and protocols

This book provides the immune oncology (IO) community with a deeper understanding of the scope of the biomarker methods to potentially improve the outcome from immunotherapy. The editors secured the input from experts in the field dedicated to translating scientific research from bench to bedside was submitted. The book provides not only details about the technical, standardization and interpretation aspects of the methods but also introduces the reader to the background information and scientific justification for selected biomarkers and assays. 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. Front Matter ....Pages i-xviii Front Matter ....Pages 1-1 Status of Immune Oncology: Challenges and Opportunities (Alessandra Cesano, Francesco M. Marincola, Magdalena Thurin)....Pages 3-21 Immunological Targets for Immunotherapy: Inhibitory T Cell Receptors (Diwakar Davar, Hassane M. Zarour)....Pages 23-60 Front Matter ....Pages 61-61 Measuring Tumor Mutational Burden Using Whole-Exome Sequencing (Tomas Vilimas)....Pages 63-91 Germline Genetics in Immuno-oncology: From Genome-Wide to Targeted Biomarker Strategies (Tomas Kirchhoff, Robert Ferguson)....Pages 93-117 Detection of Microsatellite Instability Biomarkers via Next-Generation Sequencing (Russell Bonneville, Melanie A. Krook, Hui-Zi Chen, Amy Smith, Eric Samorodnitsky, Michele R. Wing et al.)....Pages 119-132 Genetic Instability Markers in Cancer (Giuseppe Palmieri, Milena Casula, Antonella Manca, Grazia Palomba, Maria Cristina Sini, Valentina Doneddu et al.)....Pages 133-154 Validation of Circulating Tumor DNA Assays for Detection of Metastatic Melanoma (Mahrukh M. Syeda, Jennifer M. Wiggins, Broderick Corless, Cindy Spittle, George Karlin-Neumann, David Polsky)....Pages 155-180 Techniques Associated with Exosome Isolation for Biomarker Development: Liquid Biopsies for Ovarian Cancer Detection (Shayna Sharma, Carlos Salomon)....Pages 181-199 Front Matter ....Pages 201-201 Identifying MicroRNA Pathway Variants as Biomarkers of Patient Selection for Immune Therapy (Joanne B. Weidhaas)....Pages 203-212 Histone Modifications as Biomarkers for Immunotherapy (Erin M. Taylor, Brian Koss, Lauren E. Davis, Alan J. Tackett)....Pages 213-228 Front Matter ....Pages 229-229 Functional Genome Profiling to Understand Cancer Immune Responsiveness (Ena Wang, Davide Bedognetti, Francesco M. Marincola)....Pages 231-244 Using RNA Sequencing to Characterize the Tumor Microenvironment (C. C. Smith, L. M. Bixby, K. L. Miller, S. R. Selitsky, D. S. Bortone, K. A. Hoadley et al.)....Pages 245-272 Development of Gene Expression-Based Biomarkers on the nCounter® Platform for Immuno-Oncology Applications (Sarah Warren, Patrick Danaher, Afshin Mashadi-Hossein, Lynell Skewis, Brett Wallden, Sean Ferree et al.)....Pages 273-300 The CRISPR System and Cancer Immunotherapy Biomarkers (Vitaly Balan, Jianbin Wang)....Pages 301-322 Front Matter ....Pages 323-323 HLA Class I Antigen Processing Machinery Defects in Cancer Cells—Frequency, Functional Significance, and Clinical Relevance with Special Emphasis on Their Role in T Cell-Based Immunotherapy of Malignant Disease (Barbara Seliger, Soldano Ferrone)....Pages 325-350 High-Parameter Immune Profiling with CyTOF (Bita Sahaf, Adeeb Rahman, Holden T. Maecker, Sean C. Bendall)....Pages 351-368 The Adaptome as Biomarker for Assessing Cancer Immunity and Immunotherapy (Jian Han, Michael T. Lotze)....Pages 369-397 Single-Molecule Arrays for Ultrasensitive Detection of Blood-Based Biomarkers for Immunotherapy (Limor Cohen, Alissa Keegan, David R. Walt)....Pages 399-412 Single-Cell Multiplexed Proteomics on the IsoLight Resolves Cellular Functional Heterogeneity to Reveal Clinical Responses of Cancer Patients to Immunotherapies (Dong Liu, Patrick Paczkowski, Sean Mackay, Colin Ng, Jing Zhou)....Pages 413-431 Methods to Detect Immunogenic Cell Death In Vivo (Takahiro Yamazaki, Aitziber Buqué, Marissa Rybstein, Jonathan Chen, Ai Sato, Lorenzo Galluzzi)....Pages 433-452 Front Matter ....Pages 453-453 Overview of Tissue Imaging Methods (Sanjay S. Patel, Scott J. Rodig)....Pages 455-465 Multiplex Immunofluorescence Assays (Alejandro Francisco-Cruz, Edwin Roger Parra, Michael T. Tetzlaff, Ignacio I. Wistuba)....Pages 467-495 Multiplexed Immunohistochemical Consecutive Staining on Single Slide (MICSSS): Multiplexed Chromogenic IHC Assay for High-Dimensional Tissue Analysis (Guray Akturk, Robert Sweeney, Romain Remark, Miriam Merad, Sacha Gnjatic)....Pages 497-519 Cyclic Multiplexed-Immunofluorescence (cmIF), a Highly Multiplexed Method for Single-Cell Analysis (Jennifer Eng, Guillaume Thibault, Shiuh-Wen Luoh, Joe W. Gray, Young Hwan Chang, Koei Chin)....Pages 521-562 High-Plex Spatially Resolved RNA and Protein Detection Using Digital Spatial Profiling: A Technology Designed for Immuno-oncology Biomarker Discovery and Translational Research (Joseph M. Beechem)....Pages 563-583 The InSituPlex® Staining Method for Multiplexed Immunofluorescence Cell Phenotyping and Spatial Profiling of Tumor FFPE Samples (Mael Manesse, Katir K. Patel, Mark Bobrow, Sean R. Downing)....Pages 585-592 Front Matter ....Pages 593-593 Microbiome as an Immunological Modifier (Manoj Kumar, Parul Singh, Selvasankar Murugesan, Marie Vetizou, John McCulloch, Jonathan H. Badger et al.)....Pages 595-638 Front Matter ....Pages 639-639 Systems Biology for Multiplatform Data Integration: An Overview (Elad Ziv)....Pages 641-647 Bioinformatics Tools and Resources for Cancer Immunotherapy Study (Alida Palmisano, Julia Krushkal, Ming-Chung Li, Jianwen Fang, Dmitriy Sonkin, George Wright et al.)....Pages 649-678 Multiplatform Integrative Analysis of Immunogenomic Data for Biomarker Discovery (Vésteinn Thorsson)....Pages 679-698 Front Matter ....Pages 699-699 Translating Immuno-oncology Biomarkers to Diagnostic Tests: A Regulatory Perspective (You Li, Janaki Veeraraghavan, Reena Philip)....Pages 701-716 Correction to: Methods to Detect Immunogenic Cell Death In Vivo (Takahiro Yamazaki, Aitziber Buqué, Marissa Rybstein, Jonathan Chen, Ai Sato, Lorenzo Galluzzi)....Pages C1-C1 Back Matter ....Pages 717-733