Main description:

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.

Contents:

Part I: Scientific Questions and the Status of Inhibitory Receptors for Immunotherapy 1. Status of Immune-oncology: Challenges and Opportunities

Alessandra Cesano, Francesco M Marincola, and Magdalena Thurin

2. Immunological Targets for Immunotherapy: Inhibitory T Cell Receptors

Diwakar Davar and Hassane M. Zarour

Part II : Mutational and Germline Profiling 3. Measuring Tumor Mutational Burden Using Whole Exome Sequencing

Tomas 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 Sequencing

Russell 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 Melanoma

Mahrukh 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 Detection

Shayna Sharma and Carlos Salomon

Part III: Epigenetic Profiling 9. Identifying MicroRNA Pathway Variants as Biomarkers of Patient Selection for Immune Therapy

Joanne B. Weidhaas

10. Histone Modifications as Biomarkers for Immunotherapy

Erin 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 Microenvironment

Smith 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 Applications

Sarah Warren, Patrick Danaher, Afshin Mashadi-Hossein, Lynell Skewis, Brett Wallden, Sean Ferree, and Alessandra Cesano

14. The CRISPR System and Cancer Immunotherapy Biomarkers

Vitaly 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 Disease

Barbara Seliger and Soldano Ferrone

16. High-parameter Immune Profiling with CyTOF

Bita Sahaf, Adeeb Rahman, Holden T. Maecker, and Sean Bendall

17. The Adaptome as Biomarker for Assessing Cancer Immunity and Immunotherapy

Jian 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 Immunotherapies

Dong Liu, Patrick Paczkowski, Sean Mackay, Colin Ng, and Jing Zhou

20. Methods to Detect Immunogenic Cell Death in vivo

Takahiro Yamazaki, Aitziber Buque Martinez, Marissa Rybstein, Jonathan Chen, Ai Sato, and Lorenzo Galluzzi

Part VI: Tissue Imaging Methods 21. Overview of Tissue Imaging Methods

Sanjay S. Patel and Scott J. Rodig

22. Multiplex Immunofluorescence Assays

Alejandro 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 Analysis

Jennifer 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 Research

Joseph M. Beechem

26. The InSituPlex (R) Staining Method for Multiplexed Immunofluorescence Cell Phenotyping and Spatial Profiling of Tumor FFPE Samples

Mael Manesse, Katir K. Patel, Sean R. Downing, andMark Bobrow

Part VII: Microbiome 27. Microbiome as an Immunological Modifier

Manoj 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 Study

Alida 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 Discovery

Vesteinn Thorsson

Part IX: Regulatory Perspective 31. Translating Immuno-Oncology Biomarkers to Diagnostic tests: A Regulatory Perspective

You Li, Janaki Veeraraghavan, and Reena Philip