Cited by 697Histone Deacetylase Inhibitors ResearchGenomics and Chromatin DynamicsEpigenetics and DNA Methylation

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HDACs, histone deacetylation and gene transcription: from molecular biology to cancer therapeutics

Gallinari, Paola, Marco, Stefania Di, Jones, Phillip, Pallaoro, Michele, Steinkühler, Christian·2007·Cell Research

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Abstract

Histone deacetylases (HDACs) and histone acetyl transferases (HATs) are two counteracting enzyme families whose enzymatic activity controls the acetylation state of protein lysine residues, notably those contained in the N-terminal extensions of the core histones. Acetylation of histones affects gene expression through its influence on chromatin conformation. In addition, several non-histone proteins are regulated in their stability or biological function by the acetylation state of specific lysine residues. HDACs intervene in a multitude of biological processes and are part of a multiprotein family in which each member has its specialized functions. In addition, HDAC activity is tightly controlled through targeted recruitment, protein-protein interactions and post-translational modifications. Control of cell cycle progression, cell survival and differentiation are among the most important roles of these enzymes. Since these processes are affected by malignant transformation, HDAC inhibitors were developed as antineoplastic drugs and are showing encouraging efficacy in cancer patients.

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Background
HDAC1 in the Ovarian Granulosa Cells of Tan Sheep Improves Cumulus Cell Expansion and Oocyte Maturation Independently of the EGF-like Growth Factors
Xu, Y., Fan, S., Liu, Y., Shi, J., Xie, X., Wang, X., Wang, C., Liu, X., & Xia, G. (2022) · Biology · doi:10.3390/biology11101464 · Cited by 12
How to improve the clinical outcome of round spermatid injection (ROSI) into the oocyte: Correction of epigenetic abnormalities
Tanaka, A., & Watanabe, S. (2023) · Reproductive Medicine and Biology · doi:10.1002/rmb2.12503 · Cited by 12
An inhibitor screen identifies histone-modifying enzymes as mediators of polymer-mediated transgene expression from plasmid DNA
Christensen, M. D., Nitiyanandan, R., Meraji, S., Daer, R., Godeshala, S., Goklany, S., Haynes, K. A., & Rege, K. (2018) · Journal of Controlled Release · doi:10.1016/j.jconrel.2018.06.030 · Cited by 12
Emerging role of histone deacetylase inhibitors in the treatment of diffuse large B-cell lymphoma
Wang, M., Fang, X., & Wang, X. (2019) · Leukemia & lymphoma/Leukemia and lymphoma · doi:10.1080/10428194.2019.1691194 · Cited by 12
De novo missense variants in HDAC3 leading to epigenetic machinery dysfunction are associated with a variable neurodevelopmental disorder
Yoon, J. G., Lim, S.-K., Seo, H., Lee, S., Cho, J., Kim, S. Y., Koh, H. Y., Poduri, A., Ramakumaran, V. S., Vasudevan, P. C., et al. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.06.015 · Cited by 11
Molecular regulation and functional benefits of trophoblast syncytialization in optimizing maternal-fetal nutrient allocation
Li, Q., Zhu, Y. J., Yu, X., Shao, X., & Wang, Y. (2025) · Placenta · doi:10.1016/j.placenta.2025.06.003 · Cited by 11
Regulation and induction of fungal secondary metabolites: a comprehensive review
Prakash, S., Kumari, H., Sinha, M., & Kumar, A. (2025) · Archives of Microbiology · doi:10.1007/s00203-025-04386-0 · Cited by 11
“If these risks are not addressed, "epigenetic determinism" from unfair environments could become more entrenched (Gallinari et al. 2007; Lerner et al. 2024).”
Liquid chromatography mass spectrometry determination of mocetinostat (MGCD0103) in rat plasma and its application to a pharmacokinetic study
Ma, J., Zhang, Q., & Wang, X. (2014) · Xenobiotica · doi:10.3109/00498254.2014.897012 · Cited by 11
“…in certain cancers (Glaser et al., 2003), and treatment of tumor cells with HDAC inhibitors (HDACi) results in growth arrest, differentiation and apoptosis, promoting these enzymes as promising targets for anticancer therapy (Gallinari et al., 2007; Marks et al., 2001; Minucci & Pelicci, 2006).”
Background
Insights into novel emerging epigenetic drugs in myeloid malignancies
Chandhok, N. S., & Prébet, T. (2019) · Therapeutic Advances in Hematology · doi:10.1177/2040620719866081 · Cited by 11
Histone deacetylase inhibition by suberoylanilide hydroxamic acid: a therapeutic approach to treat human uterine leiomyoma
Carbajo‐García, M. C., García-Alcázar, Z., Corachán, A., Monleón, J., Trelis, A., Faus, A., Pellicer, A., & Ferrero, H. (2021) · Fertility and Sterility · doi:10.1016/j.fertnstert.2021.10.012 · Cited by 11
Deciphering the Role of Histone Modifications in Uterine Leiomyoma: Acetylation of H3K27 Regulates the Expression of Genes Involved in Proliferation, Cell Signaling, Cell Transport, Angiogenesis and Extracellular Matrix Formation
Carbajo‐García, M. C., de Miguel–Gómez, L., Juárez‐Barber, E., Trelis, A., Monleón, J., Pellicer, A., Flanagan, J. M., & Ferrero, H. (2022) · Biomedicines · doi:10.3390/biomedicines10061279 · Cited by 11
Transcription suppression is mediated by the HDAC1–Sin3 complex in Xenopus nucleoplasmic extract
Quaas, C. E., Lin, B., & Long, D. T. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102578 · Cited by 10
“Both HDACs and BRD proteins have been identified as attractive targets for therapeutic intervention (20, 21, 22, 23).”
Background
Cooperative effects of SAHA and VPA on NIS gene expression and proliferation of thyroid cancer cells
Puppin, C., Passon, N., Hershman, J. M., Filetti, S., Bulotta, S., Celano, M., Russo, D., & Damante, G. (2012) · Journal of Molecular Endocrinology · doi:10.1530/jme-11-0063 · Cited by 11
“HDACs, by removing acetyl groups, induce chromatin compaction and, therefore, favour gene silencing (Gallinari et al. 2007).”
Background
A combination of growth factors and cytokines alter preimplantation mouse embryo development, foetal development and gene expression profiles
Gurner, K. H., Truong, T. T., Harvey, A. J., & Gardner, D. K. (2020) · Molecular Human Reproduction · doi:10.1093/molehr/gaaa072 · Cited by 11
Oxa Analogues of Nexturastat A Demonstrate Improved HDAC6 Selectivity and Superior Antileukaemia Activity
Pflieger, M., Sönnichsen, M., Horstick‐Muche, N., Yang, J. C., Schliehe‐Diecks, J., Schöler, A., Borkhardt, A., Hamacher, A., Kassack, M. U., Hansen, F. K., et al. (2021) · ChemMedChem · doi:10.1002/cmdc.202001011 · Cited by 10
In Silico Identification of Promising New Pyrazole Derivative-Based Small Molecules for Modulating CRMP2, C-RAF, CYP17, VEGFR, C-KIT, and HDAC—Application towards Cancer Therapeutics
Bennani, F. E., Karrouchi, K., Doudach, L., Scrima, M., Rahman, N., Rastrelli, L., Tallei, T. E., Rudd, C. E., Faouzi, M. E. A., & Ansar, M. (2022) · Current Issues in Molecular Biology · doi:10.3390/cimb44110361 · Cited by 11
Disruption of histone acetylation homeostasis triggers cognitive dysfunction in experimental diabetes
Aggarwal, A., Yadav, B., Sharma, N., Kaur, R., & Rishi, V. (2023) · Neurochemistry International · doi:10.1016/j.neuint.2023.105592 · Cited by 10
Unveiling critical structural features for effective HDAC8 inhibition: a comprehensive study using quantitative read-across structure–activity relationship (q-RASAR) and pharmacophore modeling
Khatun, S., Dasgupta, I., Islam, R., Amin, S. A., Jha, T., Dhaked, D. K., & Gayen, S. (2024) · Molecular Diversity · doi:10.1007/s11030-024-10903-y · Cited by 10
“Aberrant expression of various HDACs has been implicated in numerous human disorders, including cancer, making them promising targets for therapeutic intervention across a spectrum of human malignancies [8].”
Mapping the evolution and impact of ketogenic diet research on diabetes management: a comprehensive bibliometric analysis from 2005 to 2024
Li, Z., Li, A., Liu, P., Zhang, B., & Yan, Y. (2024) · Frontiers in Nutrition · doi:10.3389/fnut.2024.1485642 · Cited by 10
“HDACs regulate gene expression by removing acetyl groups from histones (57).”
Background
Transcriptomics-informed pharmacology identifies epigenetic and cell cycle regulators that enhance AAV production
Tworig, J. M., Grafton, F., Fisher, K., Hörer, M., Reid, C. A., & Mandegar, M. A. (2024) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2024.101384 · Cited by 10
Epigenetic Modifier Drug Valproic Acid Enhances Cancer Metaphase Chromosome Elasticity and Electron Transport: An Atomic Force Microscopy Approach
Agrawal, T., Paul, D., Mishra, A., Arunkumar, G., & Rakshit, T. (2025) · JACS Au · doi:10.1021/jacsau.4c00991 · Cited by 10
Recent Insights into the Creation of Histone Deacetylase Inhibitors for the Treatment of Human Diseases
Александрович, Ю. П., Aleksandrova, Y. R., & Неганова, М. Е. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26178629 · Cited by 14
“For example, HDACs can engage a number of different corepressors that inactivate target transcription factors p53, STAT3, E2F1, NF-κ B, etc. [10,11].”
Crosstalk among the proteome, lysine phosphorylation, and acetylation in romidepsin-treated colon cancer cells
Wang, T., Chai, Y., Jia, Y., Gao, J., Peng, X., & Han, H.-F. (2016) · Oncotarget · doi:10.18632/oncotarget.10840 · Cited by 10
“FK228 exerts an antitumor effect through histone hyperacetylation and the subsequent transcription of genes that inhibit tumor growth [24, 25].”
Nucleolar Translocation of Histone Deacetylase 2 Is Involved in Regulation of Transcriptional Silencing in the Cat Germinal Vesicle1
Lee, P., Wildt, D. E., & Comizzoli, P. (2015) · Biology of Reproduction · doi:10.1095/biolreprod.115.129106 · Cited by 10
Liver-Specific Knockdown of Class IIa HDACs Has Limited Efficacy on Glucose Metabolism but Entails Severe Organ Side Effects in Mice
Ziegler, N., Raichur, S., Brunner, B., Hemmann, U., Stolte, M., Schwahn, U., Prochnow, H.-P., Metz-Weidmann, C., Tennagels, N., Margerie, D., et al. (2020) · Frontiers in Endocrinology · doi:10.3389/fendo.2020.00598 · Cited by 10
“Reverse transcription was performed using the high-capacity cDNA Reverse Transcription Kit (Applied Biosystems) and TaqMan R© Assays (Life Technologies) were used for qRT-PCR in a LightCycler 480 instrument (Roche) or ABI Prism 7900 (Thermo Fisher Scientific).”
BackgroundInfluential
Antitheilerial Activity of the Anticancer Histone Deacetylase Inhibitors
Barman, M., Kamble, S., Roy, S., Bhandari, V., Singothu, S., Dandasena, D., Suresh, A., & Sharma, P. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.759817 · Cited by 10
Inhibition of HDAC and Signal Transduction Pathways Induces Tight Junctions and Promotes Differentiation in p63-Positive Salivary Duct Adenocarcinoma
Nakano, M., Ohwada, K., Shindo, Y., Konno, T., Kohno, T., Kikuchi, S., Tsujiwaki, M., Ishii, D., Nishida, S., Kakuki, T., et al. (2022) · Cancers · doi:10.3390/cancers14112584 · Cited by 10
Activation of the intrinsic apoptosis pathway contributes to the induction of apoptosis in hepatocellular carcinoma cells by valproic acid
Yang, W., Zhao, X., Pei, F., Ji, M., Ma, W., Wang, Y., & Jiang, G. (2014) · Oncology Letters · doi:10.3892/ol.2014.2739 · Cited by 10
“However, numerous HDACIs that are currently used in the clinic, including trichostatin A (TSA), apicidin and suberoylanilide hydroxamic acid (SAHA), have been restricted due to toxicity and a short half-life (7).”
Probing the structure–activity relationship of endogenous histone deacetylase complexes with immobilized peptide‐inhibitors
Sindlinger, J., Bierlmeier, J., Geiger, L., Kramer, K., Finkemeier, I., & Schwarzer, D. (2016) · Journal of Peptide Science · doi:10.1002/psc.2875 · Cited by 10
Histone Deacetylase Inhibitors Enhance Cytotoxicity Towards Breast Tumors While Preserving the Wound-Healing Function of Adipose-Derived Stem Cells
Koko, K. R., Chang, S., Hagaman, A. L. R., Fromer, M. W., Nolan, R. S., Gaughan, J., Zhang, P., Carpenter, J. P., Brown, S. A., Matthews, M. S., et al. (2017) · Annals of Plastic Surgery · doi:10.1097/sap.0000000000001066 · Cited by 10
MMP14 Contributes to HDAC Inhibition-Induced Radiosensitization of Glioblastoma
Zhou, Y., Liu, H., Zheng, W., Chen, Q., Hu, S., Pan, Y., Bai, Y., Zhang, J., & Shao, C. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910403 · Cited by 11

Authors: Gallinari, P., Marco, S. D., Jones, P., Pallaoro, M., & Steinkühler, C.
Affiliations: Institute of Molecular Biology and Pathology (IT)
Corresponding author: Steinkühler, Christian
ORCID: Gallinari, Paola
Steinkühler, Christian
Venue: Cell Research
Publisher: Springer Science and Business Media LLC
Published: 2007-02-27
Volume: 17
Issue: 3
Pages: 195-211
ISSN: 1001-0602 (ISSN-L)
1748-7838
DOI: 10.1038/sj.cr.7310149
OpenAlex: W2031954417
Semantic Scholar: 755cb3e836171a20f267d47b6677a035efcf7c22
Cited by: 678
References: 165
Citations by year: 2026: 47 · 2025: 87 · 2024: 38 · 2023: 37 · 2022: 52 · 2021: 58 · 2020: 30 · 2019: 29 · 2018: 28 · 2017: 20 · 2016: 29 · 2015: 22 · 2014: 27 · 2013: 38 · 2012: 20
FWCI: 2.44
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Cell Research (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords: histone deacetylase, histone acetyltransferase, histone acetylation, gene transcription, chromatin conformation, histone deacetylase inhibitors, cancer therapeutics, non-histone protein acetylation, post-translational modification, cell cycle regulation, cell differentiation, malignant transformation
MeSH terms: Acetylation, Animals, Histone Deacetylases, Histones, Humans, Models, Biological, Models, Molecular, Molecular Biology, Neoplasms, Transcription, Genetic, Histone Deacetylase Inhibitors

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HDACs, histone deacetylation and gene transcription: from molecular biology to cancer therapeutics

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