Main description:

This thorough volume explores recent advances that have revolutionized the field of precision oncology. The chapters, contributed by experts in the areas of cancer systems and integrative biology, provide hands-on guidance toward developing tools to monitor spatial and temporal changes in tumors, tracking tumor markers in blood, and ultimately developing precision medicine to combat cancer in real time. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that ensures successful results.
Authoritative and informative, Cancer Systems and Integrative Biology serves as an invaluable resource for researchers, pharmaceutical scientists, and oncologists interested in expanding their knowledge base in the current developments in cancer research.

Contents:

1. Introduction: Cancer Systems and Integrative Biology

Robert Clarke

2. Genome-Wide Analysis of Palindrome Formation with Next-Generation Sequencing (GAPF-Seq) and a Bioinformatics Pipeline for Assessing De Novo Palindromes in Cancer Genomes

Michael M. Murata, Armando E. Giuliano, and Hisashi Tanaka

3. Sample Preparation and Differential Gene Expression Analysis of Human Cancer Cell Lines by RNA Sequencing

Dmitry Leshchiner, Tommy V. Vo, and Sachi Horibata

4. Generating Mitochondrial-Nuclear Exchange (MNX) Mice to Identify Mitochondrial Determinants of Cancer Metastasis

Danny R. Welch, Melissa A. Larson, Carolyn J. Vivian, and Jay L. Vivian

5. 3D Autologous Culture Method for Precision Oncology

Qian Xu, Mei Ling Yan, and Yao Tang

6. High-Plex Spatial Profiling of RNA and Protein Using Digital Spatial Profiler

Nan Wang, Xia Li, and Zhiyong Ding

7. Integration of Single Cell RNA-Sequencing and Network Analysis to Investigate Mechanism of Drug Resistance

Stephanie The, Patricia M. Schnepp, Greg Shelley, Jill M. Keller, Arvind Rao, and Evan T. Keller

8. Combination of Tissue Microarray Profiling and Multiplexed IHC Approaches to Investigate Transport Mechanism of Nucleoside Analog Drug Resistance

Debasis Nayak, Brenna Weadick, and Rajgopal Govindarajan

9. In Situ Proximity Ligation Assay to Visualize Protein-Protein Interactions in Tumor Specimens

Yasuhiro Miki, Erina Iwabuchi, and Takashi Suzuki

10. Integration of Metabolomic and Proteomic Data to Uncover Actionable Metabolic Pathways

Christian Heckendorf, Benjamin C. Blum, Weiwei Lin, Matthew L. Lawton, and Andrew Emili

11. Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes

April Sagan, Xiaojun Ma, Koushul Ramjattun, and Hatice Ulku Osmanbeyoglu

12. Mass Spectrometry-Based Tissue Imaging of the Tumor Microenvironment

Tyler Risom, Patrick Chang, Sandra Rost, and James Ziai

13. Multiplexed Immunoassay Using Quantum Dots to Monitor Proteins Secreted from Single Cells at Near-Single Molecule Resolution

Veena Y. Naveen, Tingwei Deng, Vanessa Herrera, and Jered B. Haun

14. Isolation and Identification of Plasma Extracellular Vesicles Protein Biomarkers

Michelle V. Lihon, Marco Hadisurya, Xiaofeng Wu, Anton Iliuk, and W. Andy Tao

15. Discovery of a Hidden Proinflammatory Signaling Proteome Using a Large Scale, Targeted Antibody Microarray Platform

Catherine Jozwik, Ofer Eidelman, and Meera Srivastava

16. Multiplex Fluorescent Immunohistochemistry for Preservation of Tumor Microenvironment Architecture and Spatial Relationship of Cells in Tumor Tissues

Jake J. McGue, Jacob J. Edwards, Brian D. Griffith, and Timothy L. Frankel

17. Circle Damage Sequencing for Whole-Genome Analysis of DNA Damage

Seung-Gi Jin, Jennifer Johnson, and Gerd P. Pfeifer

18. CRISPR-Directed Gene Editing as a Method to Reduce Chemoresistance in Lung Cancer Cells

Natalia Rivera-Torres, Pawel Bialk, and Eric B. Kmiec

19. Integrated In Silico Analysis of Proteogenomics and Drug Targets for Pancreatic Cancer Survival

Alakesh Bera, Digonto Chatterjee, Jack Hester, and Meera Srivastava

20. Advanced Computational Methods to Evaluate Vascular Heterogeneity in Tumor Tissue Based on Single Plane Illumination Microscopy

Felix T. Kurz and Artur Hahn

21. Illuminating DEPDC1B in Multi-Pronged Regulation of Tumor Progression

Howard E. Boudreau, Jennifer Robinson, and Usha N. Kasid

22. Single Cell and Spatial Analysis of Emergent Organoid Platforms

Aditi Kumar, Shuangyi Cai, Mayar Allam, Samuel Henderson, Melissa Ozbeyler, Lilly Saiontz, and Ahmet F. Coskun

23. Analysis of Phase-Separated Biomolecular Condensates in Cancer

Wei Li and Hao Jiang

24. Gain-of-Function Variomics and Multi-Omics Network Biology for Precision Medicine

Mark M. Li, Sharad Awasthi, Sumanta Ghosh, Nidhi Sahni, and S. Stephen Yi