Biomarkers for immunotherapy of cancer: methods and protocols [electronic resource]

  • Thurin, Magdalena , Cesano, Alessandra , Marincola, Francesco M.
  • Humana Press
  • 2020
Biomarkers for immunotherapy of cancer: methods and protocols [electronic resource]


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.


Part I: Scientific Questions and the Status of Inhibitory Receptors for Immunotherapy
1. Status of Immune-oncology: Challenges and OpportunitiesAlessandra Cesano, Francesco M Marincola, and Magdalena Thurin
2. Immunological Targets for Immunotherapy: Inhibitory T Cell ReceptorsDiwakar Davar and Hassane M. Zarour

Part II : Mutational and Germline Profiling
3. Measuring Tumor Mutational Burden Using Whole Exome SequencingTomas Vilimas
4. Germline Genetics in Immuno-Oncology: From Genome-wide to Targeted Biomarker Strategies Tomas Kirchhoff and Robert Ferguson
5. Detection of Microsatellite Instability Biomarkers via Next-generation SequencingRussell Bonneville, Melanie A. Krook, Hui-Zi Chen, Amy Smith, Eric Samorodnitsky, Michele R. Wing, Julie W. Reeser, and Sameek Roychowdhury
6. Genetic Instability Markers in Cancer Giuseppe Palmieri, Milena Casula, Antonella Manca, Grazia Palomba, Maria Cristina Sini, Valentina Doneddu , Antonio Cossu, and Maria Colombino
7. Validation of Circulating Tumor DNA Assays for Detection of Metastatic MelanomaMahrukh M Syeda, Jennifer M. Wiggins, Broderick Corless, Cindy Spittle, George Karlin-Neumann, and David Polsky
8. Techniques Associated with Exosome Isolation for Biomarker Development - Liquid Biopsies for Ovarian Cancer DetectionShayna Sharma and Carlos Salomon

Part III: Epigenetic Profiling
9. Identifying MicroRNA Pathway Variants as Biomarkers of Patient Selection for Immune TherapyJoanne B. Weidhaas
10. Histone Modifications as Biomarkers for ImmunotherapyErin M. Taylor, Brian Koss, Lauren E. Davis, and Alan J. Tackett

Part IV: Functional Genomic Profiling
11. Functional Genome Profiling to Understand Cancer Immune Responsiveness Ena Wang, Davide Bedognetti, and Francesco M Marincola
12. Using RNA-sequencing to Characterize the Tumor MicroenvironmentSmith CC, Bixby LM, Miller KL, Selitsky SR, Bortone DS, Hoadley KA, Vincent BG, and Serody JS
13. Development of Gene Expression Based Biomarkers on the nCounter (R) Platform for Immuno-Oncology ApplicationsSarah Warren, Patrick Danaher, Afshin Mashadi-Hossein, Lynell Skewis, Brett Wallden, Sean Ferree, and Alessandra Cesano
14. The CRISPR System and Cancer Immunotherapy BiomarkersVitaly Balan and Jianbin Wang

Part V: Phenotyping of Tumor and Immune Cells
15. 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 DiseaseBarbara Seliger and Soldano Ferrone
16. High-parameter Immune Profiling with CyTOFBita Sahaf, Adeeb Rahman, Holden T. Maecker, and Sean Bendall
17. The Adaptome as Biomarker for Assessing Cancer Immunity and ImmunotherapyJian Han and Michael T. Lotze
18. Single Molecule Arrays for Ultrasensitive Detection of Blood-based Biomarkers for Immunotherapy Limor Cohen, Alissa Keegan, and David R Walt
19. Single-cell Multiplexed Proteomics on the IsoLight Resolves Cellular Functional Heterogeneity to Reveal Clinical Responses of Cancer Patients to ImmunotherapiesDong Liu, Patrick Paczkowski, Sean Mackay, Colin Ng, and Jing Zhou
20. Methods to Detect Immunogenic Cell Death in vivoTakahiro Yamazaki, Aitziber Buque Martinez, Marissa Rybstein, Jonathan Chen, Ai Sato, and Lorenzo Galluzzi

Part VI: Tissue Imaging Methods
21. Overview of Tissue Imaging MethodsSanjay S. Patel and Scott J. Rodig
22. Multiplex Immunofluorescence AssaysAlejandro Francisco-Cruz, Edwin Roger Parra, Michael T. Tetzlaff, and Ignacio I. Wistuba,
23. 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, and Sacha Gnjatic
24 Cyclic Multiplexed-Immunofluorescence (cmIF), A Highly Multiplexed Method for Single-cell AnalysisJennifer Eng, Guillaume Thibault, Shiuh-Wen Luoh, Joe W. Gray, Young Hwan Chang, and Koei Chin
25. High-Plex Spatially Resolved RNA and Protein Detection using Digital Spatial Profiling: A Technology Designed for Immuno-Oncology Biomarker Discovery and Translational ResearchJoseph M. Beechem
26. The InSituPlex (R) Staining Method for Multiplexed Immunofluorescence Cell Phenotyping and Spatial Profiling of Tumor FFPE SamplesMael Manesse, Katir K. Patel, Sean R. Downing, andMark Bobrow

Part VII: Microbiome
27. Microbiome as an Immunological ModifierManoj Kumar, Parul Singh, Selvasankar Murugesan, Marie Vetizou, John McCulloch, Jonathan H. Badger, Giorgio Trinchieri, and Souhaila Al Khodor Part VIII: System Biology for Multi-platform Data Integration
28. Systems Biology for Multi-Platform Data Integration - Overview Elad Ziv
29. Bioinformatics Tools and Resources for Cancer Immunotherapy StudyAlida Palmisano, Julia Krushkal, Ming-Chung Li, Jianwen Fang, Dmitriy Sonkin, George Wright, Laura Yee, Yingdong Zhao, Lisa McShane
30. Multiplatform Integrative Analysis of Immunogenomic Data for Biomarker DiscoveryVesteinn Thorsson

Part IX: Regulatory Perspective
31. Translating Immuno-Oncology Biomarkers to Diagnostic tests: A Regulatory PerspectiveYou Li, Janaki Veeraraghavan, and Reena Philip