(PDF) Biomarkers for Immunotherapy of Cancer by Magdalena Thurin

This is the PDF eBook version for Biomarkers for Immunotherapy of Cancer – Methods and Protocols by Magdalena Thurin, Alessandra Cesano, Francesco M. Marincola

Table of 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® 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 Buqué 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 Immunohishemical 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® 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 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 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
Part IX: Regulatory Perspective
31. Translating Immuno-Oncology Biomarkers to Diagnostic tests: A Regulatory Perspective
You Li, Janaki Veeraraghavan, and Reena Philip