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.

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

3. Measuring Tumor Mutational Burden Using Whole Exome Sequencing

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

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

11. Functional Genome Profiling to Understand Cancer Immune Responsiveness

 Ena Wang, Davide Bedognetti, and Francesco M Marincola

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® Platform for Immuno-Oncology Applications

14. The CRISPR System and Cancer Immunotherapy Biomarkers

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 Buqué Martinez, Marissa Rybstein, Jonathan Chen, Ai Sato, and Lorenzo Galluzzi

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

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

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

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

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

Vésteinn Thorsson

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

You Li, Janaki Veeraraghavan, and Reena Philip