HDAC/HAT Function Assessment and Inhibitor Development: Methods and Protocols

by Oliver H. Krïmer (Editor)

Overview

This fully updated edition provides a series of methods for how best to assess functions of histone deacetylases and acetyltransferases. The disease-relevance of dysregulated protein deacetylation by overexpressed or aberrantly activated histone deacetylases has spurred an intense search for novel and improved inhibitors of these enzymes, as reflected in this collection. Expert contributors explore the generation and evaluation of novel histone deacetylase inhibitors and new and improved techniques to assess acetylation-dependent molecular mechanisms in vitro and in vivo. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory prools, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and up-to-date, HDAC/HAT Function Assessment and Inhibitor Development: Methods and Prools, Second Edition serves as an ideal guide for researchers seeking to further elucidate this vital area of study.

Product Details

ISBN-13:	9781071627907
Publisher:	Springer US
Publication date:	10/19/2023
Series:	Methods in Molecular Biology , #2589
Edition description:	Second Edition 2023
Pages:	511
Product dimensions:	7.01(w) x 10.00(h) x (d)

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