Biomarkers for Immunotherapy of Cancer: Methods and Protocols

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