Cancer Systems and Integrative Biology

ISBN-13: 9781071631621 / Angielski / Twarda / 2023

Usha N. Kasid; Robert Clarke

Opis

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.

Spis treści

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