HDAC6 inhibition disrupts HDAC6-P300 interaction reshaping the cancer chromatin landscape.
Humans
Histone Deacetylase 6
/ genetics
Chromatin
/ genetics
Cell Line, Tumor
Histone Deacetylase Inhibitors
/ pharmacology
Acetylation
/ drug effects
Neoplasms
/ drug therapy
E1A-Associated p300 Protein
/ genetics
Gene Expression Regulation, Neoplastic
/ drug effects
Cell Proliferation
/ drug effects
Histones
/ metabolism
Ubiquitination
/ drug effects
Apoptosis
Cancer
Cell cycle
Deacetylase inhibitors
HAT
HDAC
Histone acetylation
Proliferation
Tumorigenesis
Journal
Clinical epigenetics
ISSN: 1868-7083
Titre abrégé: Clin Epigenetics
Pays: Germany
ID NLM: 101516977
Informations de publication
Date de publication:
18 Aug 2024
18 Aug 2024
Historique:
received:
14
03
2024
accepted:
08
08
2024
medline:
19
8
2024
pubmed:
19
8
2024
entrez:
18
8
2024
Statut:
epublish
Résumé
Histone deacetylases (HDACs) are crucial regulators of gene expression, DNA synthesis, and cellular processes, making them essential targets in cancer research. HDAC6, specifically, influences protein stability and chromatin dynamics. Despite HDAC6's potential therapeutic value, its exact role in gene regulation and chromatin remodeling needs further clarification. This study examines how HDAC6 inactivation influences lysine acetyltransferase P300 stabilization and subsequent effects on chromatin structure and function in cancer cells. We employed the HDAC6 inhibitor ITF3756, siRNA, or CRISPR/Cas9 gene editing to inactivate HDAC6 in different epigenomic backgrounds. Constantly, this inactivation led to significant changes in chromatin accessibility, particularly increased acetylation of histone H3 lysines 9, 14, and 27 (ATAC-seq and H3K27Ac ChIP-seq analysis). Transcriptomics, proteomics, and gene ontology analysis revealed gene changes in cell proliferation, adhesion, migration, and apoptosis. Significantly, HDAC6 inactivation altered P300 ubiquitination, stabilizing P300 and leading to downregulating genes critical for cancer cell survival. Our study highlights the substantial impact of HDAC6 inactivation on the chromatin landscape of cancer cells and suggests a role for P300 in contributing to the anticancer effects. The stabilization of P300 with HDAC6 inhibition proposes a potential shift in therapeutic focus from HDAC6 itself to its interaction with P300. This finding opens new avenues for developing targeted cancer therapies, improving our understanding of epigenetic mechanisms in cancer cells.
Sections du résumé
BACKGROUND
BACKGROUND
Histone deacetylases (HDACs) are crucial regulators of gene expression, DNA synthesis, and cellular processes, making them essential targets in cancer research. HDAC6, specifically, influences protein stability and chromatin dynamics. Despite HDAC6's potential therapeutic value, its exact role in gene regulation and chromatin remodeling needs further clarification. This study examines how HDAC6 inactivation influences lysine acetyltransferase P300 stabilization and subsequent effects on chromatin structure and function in cancer cells.
METHODS AND RESULTS
RESULTS
We employed the HDAC6 inhibitor ITF3756, siRNA, or CRISPR/Cas9 gene editing to inactivate HDAC6 in different epigenomic backgrounds. Constantly, this inactivation led to significant changes in chromatin accessibility, particularly increased acetylation of histone H3 lysines 9, 14, and 27 (ATAC-seq and H3K27Ac ChIP-seq analysis). Transcriptomics, proteomics, and gene ontology analysis revealed gene changes in cell proliferation, adhesion, migration, and apoptosis. Significantly, HDAC6 inactivation altered P300 ubiquitination, stabilizing P300 and leading to downregulating genes critical for cancer cell survival.
CONCLUSIONS
CONCLUSIONS
Our study highlights the substantial impact of HDAC6 inactivation on the chromatin landscape of cancer cells and suggests a role for P300 in contributing to the anticancer effects. The stabilization of P300 with HDAC6 inhibition proposes a potential shift in therapeutic focus from HDAC6 itself to its interaction with P300. This finding opens new avenues for developing targeted cancer therapies, improving our understanding of epigenetic mechanisms in cancer cells.
Identifiants
pubmed: 39155390
doi: 10.1186/s13148-024-01725-8
pii: 10.1186/s13148-024-01725-8
doi:
Substances chimiques
Histone Deacetylase 6
EC 3.5.1.98
HDAC6 protein, human
EC 3.5.1.98
Chromatin
0
Histone Deacetylase Inhibitors
0
E1A-Associated p300 Protein
EC 2.3.1.48
EP300 protein, human
EC 2.3.1.48
Histones
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
109Informations de copyright
© 2024. The Author(s).
Références
Milazzo G, Mercatelli D, Di Muzio G, Triboli L, De Rosa P, Perini G, et al. Histone deacetylases (HDACs): evolution, specificity, role in transcriptional complexes, and pharmacological actionability. Genes (Basel). 2020;11(5):556.
pubmed: 32429325
doi: 10.3390/genes11050556
Hubbert C, Guardiola A, Shao R, Kawaguchi Y, Ito A, Nixon A, et al. HDAC6 is a microtubule-associated deacetylase. Nature. 2002;417(6887):455–8.
pubmed: 12024216
doi: 10.1038/417455a
Zhang X, Yuan Z, Zhang Y, Yong S, Salas-Burgos A, Koomen J, et al. HDAC6 modulates cell motility by altering the acetylation level of cortactin. Mol Cell. 2007;27(2):197–213.
pubmed: 17643370
pmcid: 2684874
doi: 10.1016/j.molcel.2007.05.033
Lin YH, Major JL, Liebner T, Hourani Z, Travers JG, Wennersten SA, et al. HDAC6 modulates myofibril stiffness and diastolic function of the heart. J Clin Invest. 2022;132:10.
doi: 10.1172/JCI148333
Kovacs JJ, Murphy PJ, Gaillard S, Zhao X, Wu JT, Nicchitta CV, et al. HDAC6 regulates Hsp90 acetylation and chaperone-dependent activation of glucocorticoid receptor. Mol Cell. 2005;18(5):601–7.
pubmed: 15916966
doi: 10.1016/j.molcel.2005.04.021
Fusco C, Micale L, Augello B, Mandriani B, Pellico MT, De Nittis P, et al. HDAC6 mediates the acetylation of TRIM50. Cell Signal. 2014;26(2):363–9.
pubmed: 24308962
doi: 10.1016/j.cellsig.2013.11.036
Li L, Yang XJ. Tubulin acetylation: responsible enzymes, biological functions and human diseases. Cell Mol Life Sci. 2015;72(22):4237–55.
pubmed: 26227334
pmcid: 11113413
doi: 10.1007/s00018-015-2000-5
Li Y, Shin D, Kwon SH. Histone deacetylase 6 plays a role as a distinct regulator of diverse cellular processes. FEBS J. 2013;280(3):775–93.
pubmed: 23181831
doi: 10.1111/febs.12079
Yang Y, Rao R, Shen J, Tang Y, Fiskus W, Nechtman J, et al. Role of acetylation and extracellular location of heat shock protein 90alpha in tumor cell invasion. Cancer Res. 2008;68(12):4833–42.
pubmed: 18559531
pmcid: 2665713
doi: 10.1158/0008-5472.CAN-08-0644
Sadoul K, Boyault C, Pabion M, Khochbin S. Regulation of protein turnover by acetyltransferases and deacetylases. Biochimie. 2008;90(2):306–12.
pubmed: 17681659
doi: 10.1016/j.biochi.2007.06.009
Xu Y, Wan W. Acetylation in the regulation of autophagy. Autophagy. 2023;19(2):379–87.
pubmed: 35435793
doi: 10.1080/15548627.2022.2062112
Valenzuela-Fernandez A, Cabrero JR, Serrador JM, Sanchez-Madrid F. HDAC6: a key regulator of cytoskeleton, cell migration and cell-cell interactions. Trends Cell Biol. 2008;18(6):291–7.
pubmed: 18472263
doi: 10.1016/j.tcb.2008.04.003
Tsujimoto K, Jo T, Nagira D, Konaka H, Park JH, Yoshimura SI, et al. The lysosomal ragulator complex activates NLRP3 inflammasome in vivo via HDAC6. EMBO J. 2023;42(1): e111389.
pubmed: 36444797
doi: 10.15252/embj.2022111389
Kulthinee S, Yano N, Zhuang S, Wang L, Zhao TC. Critical Functions of histone deacetylases (HDACs) in modulating inflammation associated with cardiovascular diseases. Pathophysiology. 2022;29(3):471–85.
pubmed: 35997393
pmcid: 9397025
doi: 10.3390/pathophysiology29030038
Seidel C, Schnekenburger M, Dicato M, Diederich M. Histone deacetylase 6 in health and disease. Epigenomics. 2015;7(1):103–18.
pubmed: 25687470
doi: 10.2217/epi.14.69
Chen J, Li Q. Life and death of transcriptional co-activator p300. Epigenetics. 2011;6(8):957–61.
pubmed: 21730760
doi: 10.4161/epi.6.8.16065
Ghosh AK. Acetyltransferase p300 Is a putative epidrug target for amelioration of cellular aging-related cardiovascular disease. Cells. 2021;10:11.
doi: 10.3390/cells10112839
Sun H, Yang X, Zhu J, Lv T, Chen Y, Chen G, et al. Inhibition of p300-HAT results in a reduced histone acetylation and down-regulation of gene expression in cardiac myocytes. Life Sci. 2010;87(23–26):707–14.
pubmed: 21034749
doi: 10.1016/j.lfs.2010.10.009
Lu P, Xu Y, Sheng ZY, Peng XG, Zhang JJ, Wu QH, et al. De-ubiquitination of p300 by USP12 critically enhances METTL3 expression and Ang II-induced cardiac hypertrophy. Exp Cell Res. 2021;406(1): 112761.
pubmed: 34339675
doi: 10.1016/j.yexcr.2021.112761
Girdwood D, Bumpass D, Vaughan OA, Thain A, Anderson LA, Snowden AW, et al. P300 transcriptional repression is mediated by SUMO modification. Mol Cell. 2003;11(4):1043–54.
pubmed: 12718889
doi: 10.1016/S1097-2765(03)00141-2
Sankar N, Baluchamy S, Kadeppagari RK, Singhal G, Weitzman S, Thimmapaya B. p300 provides a corepressor function by cooperating with YY1 and HDAC3 to repress c-Myc. Oncogene. 2008;27(43):5717–28.
pubmed: 18542060
doi: 10.1038/onc.2008.181
Bobrowska A, Paganetti P, Matthias P, Bates GP. Hdac6 knock-out increases tubulin acetylation but does not modify disease progression in the R6/2 mouse model of Huntington’s disease. PLoS ONE. 2011;6(6): e20696.
pubmed: 21677773
pmcid: 3108987
doi: 10.1371/journal.pone.0020696
Han Y, Jeong HM, Jin YH, Kim YJ, Jeong HG, Yeo CY, et al. Acetylation of histone deacetylase 6 by p300 attenuates its deacetylase activity. Biochem Biophys Res Commun. 2009;383(1):88–92.
pubmed: 19344692
doi: 10.1016/j.bbrc.2009.03.147
Liu Y, Peng L, Seto E, Huang S, Qiu Y. Modulation of histone deacetylase 6 (HDAC6) nuclear import and tubulin deacetylase activity through acetylation. J Biol Chem. 2012;287(34):29168–74.
pubmed: 22778253
pmcid: 3436516
doi: 10.1074/jbc.M112.371120
Getsy PM, Coffee GA, Kelley TJ, Lewis SJ. Male histone deacetylase 6 (HDAC6) knock-out mice have enhanced ventilatory responses to hypoxic challenge. Res Sq. 2023;14:1332810.
Dallavalle S, Pisano C, Zunino F. Development and therapeutic impact of HDAC6-selective inhibitors. Biochem Pharmacol. 2012;84(6):756–65.
pubmed: 22728920
doi: 10.1016/j.bcp.2012.06.014
Zhao Y, Liang T, Hou X, Fang H. Recent development of novel HDAC6 isoform-selective inhibitors. Curr Med Chem. 2021;28(21):4133–51.
pubmed: 33176627
doi: 10.2174/0929867327666201111142653
Ripamonti C, Spadotto V, Pozzi P, Stevenazzi A, Vergani B, Marchini M, et al. HDAC inhibition as potential therapeutic strategy to restore the deregulated immune response in severe COVID-19. Front Immunol. 2022;13: 841716.
pubmed: 35592335
pmcid: 9111747
doi: 10.3389/fimmu.2022.841716
Vergani B, Sandrone G, Marchini M, Ripamonti C, Cellupica E, Galbiati E, et al. Novel benzohydroxamate-based potent and selective histone deacetylase 6 (HDAC6) inhibitors bearing a pentaheterocyclic scaffold: design, synthesis, and biological evaluation. J Med Chem. 2019;62(23):10711–39.
pubmed: 31710483
doi: 10.1021/acs.jmedchem.9b01194
Elsasser S, Schmidt M, Finley D. Characterization of the proteasome using native gel electrophoresis. Methods Enzymol. 2005;398:353–63.
pubmed: 16275342
doi: 10.1016/S0076-6879(05)98029-4
Sbardella D, Tundo GR, Coletta M, Manni G, Oddone F. Dexamethasone downregulates autophagy through accelerated turnover of the Ulk-1 complex in a trabecular meshwork cells strain: insights on steroid-induced glaucoma pathogenesis. Int J Mol Sci. 2021;22(11):5891.
pubmed: 34072647
pmcid: 8198647
doi: 10.3390/ijms22115891
Milite C, Feoli A, Sasaki K, La Pietra V, Balzano AL, Marinelli L, et al. A novel cell-permeable, selective, and noncompetitive inhibitor of KAT3 histone acetyltransferases from a combined molecular pruning/classical isosterism approach. J Med Chem. 2015;58(6):2779–98.
pubmed: 25730130
doi: 10.1021/jm5019687
Slaughter MJ, Shanle EK, Khan A, Chua KF, Hong T, Boxer LD, et al. HDAC inhibition results in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies. Cell Rep. 2021;34(3): 108638.
pubmed: 33472068
pmcid: 7886050
doi: 10.1016/j.celrep.2020.108638
Kim SH, Kang HJ, Na H, Lee MO. Trichostatin A enhances acetylation as well as protein stability of ERalpha through induction of p300 protein. Breast Cancer Res. 2010;12(2):R22.
pubmed: 20388208
pmcid: 2879569
doi: 10.1186/bcr2562
Jain S, Wei J, Mitrani LR, Bishopric NH. Auto-acetylation stabilizes p300 in cardiac myocytes during acute oxidative stress, promoting STAT3 accumulation and cell survival. Breast Cancer Res Treat. 2012;135(1):103–14.
pubmed: 22562121
doi: 10.1007/s10549-012-2069-6
Ryan CM, Harries JC, Kindle KB, Collins HM, Heery DM. Functional interaction of CREB binding protein (CBP) with nuclear transport proteins and modulation by HDAC inhibitors. Cell Cycle. 2006;5(18):2146–52.
pubmed: 16969114
doi: 10.4161/cc.5.18.3207
Choi JR, Lee SY, Shin KS, Choi CY, Kang SJ. p300-mediated acetylation increased the protein stability of HIPK2 and enhanced its tumor suppressor function. Sci Rep. 2017;7(1):16136.
pubmed: 29170424
pmcid: 5701035
doi: 10.1038/s41598-017-16489-w
Delcuve GP, Khan DH, Davie JR. Roles of histone deacetylases in epigenetic regulation: emerging paradigms from studies with inhibitors. Clin Epigenetics. 2012;4(1):5.
pubmed: 22414492
pmcid: 3320549
doi: 10.1186/1868-7083-4-5
Wang P, Wang Z, Liu J. Role of HDACs in normal and malignant hematopoiesis. Mol Cancer. 2020;19(1):5.
pubmed: 31910827
pmcid: 6945581
doi: 10.1186/s12943-019-1127-7
Black JC, Mosley A, Kitada T, Washburn M, Carey M. The SIRT2 deacetylase regulates autoacetylation of p300. Mol Cell. 2008;32(3):449–55.
pubmed: 18995842
pmcid: 2645867
doi: 10.1016/j.molcel.2008.09.018
Han Y, Jin YH, Kim YJ, Kang BY, Choi HJ, Kim DW, et al. Acetylation of Sirt2 by p300 attenuates its deacetylase activity. Biochem Biophys Res Commun. 2008;375(4):576–80.
pubmed: 18722353
doi: 10.1016/j.bbrc.2008.08.042
Bachman M, Uribe-Lewis S, Yang X, Burgess HE, Iurlaro M, Reik W, et al. 5-Formylcytosine can be a stable DNA modification in mammals. Nat Chem Biol. 2015;11(8):555–7.
pubmed: 26098680
pmcid: 5486442
doi: 10.1038/nchembio.1848
Bachman M, Uribe-Lewis S, Yang X, Williams M, Murrell A, Balasubramanian S. 5-Hydroxymethylcytosine is a predominantly stable DNA modification. Nat Chem. 2014;6(12):1049–55.
pubmed: 25411882
pmcid: 4382525
doi: 10.1038/nchem.2064
Zhang QQ, Zhang WJ, Chang S. HDAC6 inhibition: a significant potential regulator and therapeutic option to translate into clinical practice in renal transplantation. Front Immunol. 2023;14:1168848.
pubmed: 37545520
pmcid: 10401441
doi: 10.3389/fimmu.2023.1168848
Li T, Zhang C, Hassan S, Liu X, Song F, Chen K, et al. Histone deacetylase 6 in cancer. J Hematol Oncol. 2018;11(1):111.
pubmed: 30176876
pmcid: 6122547
doi: 10.1186/s13045-018-0654-9
Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc. 2022;17(6):1518–52.
pubmed: 35478247
pmcid: 9189070
doi: 10.1038/s41596-022-00692-9
Jo H, Shim K, Jeoung D. Targeting HDAC6 to overcome autophagy-promoted anticancer drug resistance. Int J Mol Sci. 2022;23(17):9592.
pubmed: 36076996
pmcid: 9455701
doi: 10.3390/ijms23179592
Aguilar-Medina M, Avendano-Felix M, Lizarraga-Verdugo E, Bermudez M, Romero-Quintana JG, Ramos-Payan R, et al. SOX9 stem-cell factor: clinical and functional relevance in cancer. J Oncol. 2019;2019:6754040.
pubmed: 31057614
pmcid: 6463569
doi: 10.1155/2019/6754040
Yang W, Feng Y, Zhou J, Cheung OK, Cao J, Wang J, et al. A selective HDAC8 inhibitor potentiates antitumor immunity and efficacy of immune checkpoint blockade in hepatocellular carcinoma. Sci Transl Med. 2021;13(588):6804.
doi: 10.1126/scitranslmed.aaz6804
Vanaja GR, Ramulu HG, Kalle AM. Overexpressed HDAC8 in cervical cancer cells shows functional redundancy of tubulin deacetylation with HDAC6. Cell Commun Signal. 2018;16(1):20.
pubmed: 29716651
pmcid: 5930436
doi: 10.1186/s12964-018-0231-4
Iida M, Harari PM, Wheeler DL, Toulany M. Targeting AKT/PKB to improve treatment outcomes for solid tumors. Mutat Res. 2020;819–820: 111690.
pubmed: 32120136
pmcid: 7169978
doi: 10.1016/j.mrfmmm.2020.111690
Pascual J, Turner NC. Targeting the PI3-kinase pathway in triple-negative breast cancer. Ann Oncol. 2019;30(7):1051–60.
pubmed: 31050709
doi: 10.1093/annonc/mdz133
Jin Q, Yu LR, Wang L, Zhang Z, Kasper LH, Lee JE, et al. Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO J. 2011;30(2):249–62.
pubmed: 21131905
doi: 10.1038/emboj.2010.318
Wang M, Chen Z, Zhang Y. CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos. EMBO J. 2022;41(22): e112012.
pubmed: 36215692
pmcid: 9670200
doi: 10.15252/embj.2022112012
Cai LY, Chen SJ, Xiao SH, Sun QJ, Ding CH, Zheng BN, et al. Targeting p300/CBP attenuates hepatocellular carcinoma progression through epigenetic regulation of metabolism. Cancer Res. 2021;81(4):860–72.
pubmed: 33361394
doi: 10.1158/0008-5472.CAN-20-1323
Benedetti R, Conte M, Iside C, Altucci L. Epigenetic-based therapy: from single- to multi-target approaches. Int J Biochem Cell Biol. 2015;69:121–31.
pubmed: 26494003
doi: 10.1016/j.biocel.2015.10.016
Kaur S, Rajoria P, Chopra M. HDAC6: a unique HDAC family member as a cancer target. Cell Oncol (Dordr). 2022;45(5):779–829.
pubmed: 36036883
doi: 10.1007/s13402-022-00704-6