Table of Contents
Part I: In Vivo and 3R Models to Assess HDAC Functions and Effects of HDACi 1. Analyzing Lymphoma Development and Progression Using HDACi in Mouse Models
Eva-Maria Piskor, René Winkler, and Christian Kosan
2. Colony Formation Assay to Test the Impact of HDACi on Leukemic Cells
Miriam Pons and Mandy Beyer
3. Defined Human Leukemic CD34+ Liquid Cultures to Study HDAC/Transcriptional Repressor Complexes
Roland Windisch, Sophie Kreissig, and Christian Wichmann
4. Development of a Cellular Model Mimicking Specific HDAC Inhibitors
Lena Hess, Verena Moos, and Christian Seiser
5. Evaluation of Anti-Tumor and On-Target Activity of HDAC Inhibitors with the Zebrafish Embryo Xenograft Model
Charlotte Gatzweiler, Johannes Ridinger, Simay Ayhan, Sara Najafi, Heike Peterziel, Olaf Witt, and Ina Oehme
6. Human Platelet Lysate as Valid Cell Growth Additive to Assess Protein Acetylation
Miriam Pons, Roland Conradi, Walburgis Brenner, and Oliver H. Krämer
7. Investigating Physiopathological Roles for Sirtuins in a Mouse Model
Shimin Sun, Xiaojiao Xia, Ming Wang, and Baohua Liu
8. Patient-Derived Organoids for In Vivo Validation of In Vitro Data
Said Kdimati, Florian Bürtin, Michael Linnebacher, and Christina Susanne Mullins
Part II: Novel HDAC Inhibitors and Improved Formulations for HDAC Inhibitors
9. Analysis of HDACi-Coupled Nanoparticles: Opportunities and Challenges
Marie Kühne, Susanne Hofmann, Henry Lindemann, Zoltán Cseresnyés, Andreas Dzierza, Daniel Schröder, Maren Godmann, Andreas Koschella, Christian Eggeling, Dagmar Fischer, Marc Thilo Figge, Thomas Heinze, and Thorsten Heinzel
10. Development of Pyrazine-Anilinobenzamides as Histone Deacetylase HDAC1-3 Selective Inhibitors and Biological Testing Against Pancreas Cancer Cell Lines
Mohamed Abdelsalam, Hany S. Ibrahim, Lukas Krauss, Matthes Zessin, Anita Vecchio, Sieglinde Hastreiter, Mike Schutkowski, Günter Schneider, and Wolfgang Sippl
11. Evaluation of Small Molecule HDAC Inhibitors through In Vitro and In Cellulo Approaches
Nabanita Nawar, Harsimran Kaur Garcha, Abootaleb Sedighi, Elvin D. de Araujo, and Patrick T. Gunning
12. Synthesis, Biochemical, and Cellular Evaluation of HDAC6 Targeting Proteolysis Targeting Chimeras
Salma Darwish, Tino Heimburg, Johannes Ridinger, Daniel Herp, Matthias Schmidt, Christophe Romier, Manfred Jung, Ina Oehme, and Wolfgang Sippl
13. HDACi Delivery Systems Based on Cellulose Valproate Nanoparticles
Henry Lindemann, Marie Kühne, Andreas Koschella, Maren Godmann, Thorsten Heinzel, and Thomas Heinze
14. Synthesis and Characterization of Reversible Covalent HDAC4 Inhibitors
Anton Frühauf, Benjamin Wolff, Markus Schweipert, and Franz-Josef Meyer-Almes
Part III: Innovative Techniques to Determine the Impact of Acetylation on Chromatin, DNA Damage, and Cell Stress Responses
15. Analysis of Cell Cycle and DNA Compaction Dependent Subnuclear Distribution of Histone Marks
Sunil Kumar Pradhan and M. Cristina Cardoso
16. Analyzing the Effects of HDAC Inhibitors on DNA Damage and Associated Cytotoxicity in Primary Hepaytes
Max J. Carlsson and Jörg Fahrer
17. Assessment of HDAC Inhibitor-Induced Endoplasmic Reticulum (ER) Stress
Melisa Halilovic, Lisa Marx-Blümel, Christian Marx, Katrin Buder, James F. Beck, and Jürgen Sonnemann
18. Assessment of Mihondrial Dysfunctions after Sirtuin Inhibition
Christian Marx, Lisa Marx-Blümel, Jürgen Sonnemann, and Zhao-Qi Wang
19. Assessing the Effect of Histone Deacetylase Inhibitors on DNA Double-Strand Break Repair by Non-Homologous End Joining
Oliver H. Krämer, Tamara Diehl, and Wynand P. Roos
20. Assessing SIRT7 Activity In Vivo and In Vitro in Response to DNA Damage
Arif Ali Chishti, Zhenhai Li, Baohua Liu, and Wei-Guo Zhu
21. Methods to Evaluate the Effects of HAT/KAT Inhibition on SIAH2-Driven Reactive Oxygen Species Generation in Helicobacter pylori-Infected Gastric Epithelial Cells
Pragyesh Dixit, Shrikant Babanrao Kokate, Suvasmita Rath, Lopamudra Das, Debashish Chakraborty, and Asima Bhattacharyya
22. Monitoring Changes in Intracellular Reactive Oxygen Species Levels in Response to Histone Deacetylase Inhibitors
Al-Hassan M. Mustafa, Ramy Ashry, and Oliver H. Krämer
23. Single-Cell Analysis of Histone Acetylation Dynamics at Replication Forks Using PLA and SIRF
Seo Yun Lee, Jae Jin Kim, and Kyle M. Miller
24. Testing the Effect of Histone Acetyltransferases on Local Chromatin Compaction
Maximilian Pfisterer and M. Lienhard Schmitz
Part IV: Modern Assays to Evaluate HDAC Functions and HDACi, Including CRISPR-Cas9 Techniques
25. A Genome-Wide CRISPR-Cas9 Loss-of-Function Screening to Identify Host Restriction Factors Modulating Oncolytic Virotherapy
Michela Muscolini, John Hiscott, and Evelyne Tassone
26. Cloning Strategy for HDAC1/HDAC2 Hybrid Protein Expression in Mammalian Cells
Désirée Gül, Sandra Olf, Jan Hagemann, Roland H. Stauber, and Oliver H. Krämer
27. Continuous Histone Deacylase Activity Assays
Matthes Zessin, Marat Meleshin, Wolfgang Sippl, and Mike Schutkowski
28. CRISPR Activation/Interference Screen to Identify Genetic Networks in HDAC-Inhibitor Resistant Cells
Paul Jung, Laura Schmalbrock, and Matthias Wirth
29. Determining Potency of Inhibitors Targeting Histone Deacetylase 6 by Quantification of Acetylated Tubulin in Cells
Jana Mikesova, Marketa Ondrakova, Iva Jelinkova, Jakub Ptacek, Zora Novakova, and Cyril Barinka
30. Expression and Crystallization of HDAC6 Tandem Catalytic Domains
Gerasimos Langousis, Jacint Sanchez, Georg Kempf, and Patrick Matthias
31. Fluorescence Polarization-Based Competition Assays to Evaluate Histone Deacetylase 6 Inhibitors
Qirat F. Ashraf, Erica J. Quilates, Olasunkanmi O. Olaoye, Elvin D. de Araujo, and Patrick T. Gunning
32. Immunoprecipitation of HDAC6 and Interacting Proteins
Longlong Wang, Jacint Sanchez, Daniel Hess, and Patrick Matthias
