Cancer Drug Resistance Methods and Protocols

This volume discusses the latest techniques used to identify cancer drug resistance determinants at the molecular, cellular, and functional levels. Chapters in this book cover up-to-date topics including tumor-microenvironment cell co-culture methods and microfluidics systems; workflows for functional assessment of drug resistance in vitro and in vivo; quantitative techniques for identifying quiescent blood-flow circulating cells; and single-cell characterization methods, such as mass cytometry. 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.

Cutting-edge and practical, Cancer Drug Resistance: Methods and Protocols is a valuable resource for all scientists and researchers who are looking to learn more about the latest developments in understanding and overcoming anticancer drug resistance.  

Preface..

Table of Contents…

Contributing Authors…

1. A 3D Biomimetic System for Testing Anticancer Drugs Sensitivity

Miodrag Dragoj, Jasmina Stojkovska, Sofija Jovanovic Stojanov, Bojana Obradovic, and Milica Pešic

2. Patient-Derived Breast Cancer Tissue Cultures for Anti-Endocrine Drug Assays

Giacomo Domenici, Gonçalo Trindade, Marta F. Estrada, Ana Luísa Cartaxo, Paula M. Alves, Saudade André, and Catarina Brito

3. Co-Culture of Two Different Cell Lines in a Two-Layer Microfluidic Device

Sharif M. Rahman, Elizabeth C. Martin, and Adam T. Melvin

Hamidreza Aboulkheyr Es, Amir Reza Aref, and Majid Ebrahimi Warkiani

5. A Methodological Workflow to Analyze Synthetic Lethality and Drug Synergism in Cancer Cells Johann Gout, Elodie Roger, Alexander Kleger, and Lukas Perkhofer

Karen T. Barker and Orli Yogev

7. A Label Retaining System to Capture Slow Cycling Cancer Cells

Isabel Puig and Héctor G. Palmer

Chiara Nicolazzo and Paola Gazzaniga

9. Assessment of Tumor Heterogeneity in High-Grade Serous Ovarian Cancer: Mass Cytometry to Understand the Complex Tumor Biology

Luca Pasquini, Roberta Riccioni, and Eleonora Petrucci

10. Analysis of Transcriptomic Data Generated from Drug Treated Cancer Cell Line

Swarnima Kushwaha, Sudeshna Mukherjee, Rajdeep Chowdhury, and Shibasish Chowdhury

11. Simultaneous Mapping of Enhancers and Enhancer Rearrangements with Paired-End H3K27ac ChIP-seq

Israel Antman, Ester Davis, Shahd Abu-Kamel, Merav Hecht, and Yotam Drier

12. Identification of Drug Resistance Mechanisms using Genome-Wide CRISPR-Cas9 Screens

Graham MacLeod, Nishani Rajakulendran, and Stephane Angers

13. RNA Sequencing Data Analysis on the Maser Platform and the Tag-Count Comparison-Graphical User Interface

Kenta Ujifuku, Yoichi Morofuji, and Hiroshi Masumoto

14. Dissecting the Epigenomic Driving Drug Resistance by ATAC-Seq

Francesca de Nicola, Giacomo Corleone, and Frauke Goeman

15. Polygenomic Interrogation of Drug Resistance Genes

Robert J. Autry

16. Analysis of ER-phagy in Cancer Drug Resistance

Sandhya Chipurupalli, Vincenzo Desiderio, and Nirmal Robinson

17. Drug Target Prediction using Context-Specific Metabolic Models Reconstructed from rFastcormics

Tamara Bintener, Maria Pires Pacheco, Ali Kishk, Jeff Didier, and Thomas Sauter

Subject Index List…