Epigenetic Targets in Hepatocellular Carcinoma Cells: Identification of Chaperone Protein Complexes with Histone Deacetylases

• Bosch FX , RibesJ, CleriesR, DiazM. Epidemiology of hepatocellular carcinoma. Clin. Liver Dis.9(2) , 191–211 (2005).
   PubMedGoogle Scholar
• Ayoola EA , GadourMO. Hepatocellular carcinoma in Saudi Arabia: role of hepatitis B and C infection. J. Gastroenterol. Hepatol.19(6) , 665–669 (2004).
   PubMed Web of Science ®Google Scholar
• Hassoun Z , GoresGJ. Treatment of hepatocellular carcinoma. Clin. Gastroenterol. Hepatol.1(1) , 10–18 (2003).
   PubMed Web of Science ®Google Scholar
• Li T , WanB, HuangJ, ZhangX. Comparison of gene expression in hepatocellular carcinoma, liver development, and liver regeneration. Mol. Genet. Genomics283(5) , 485–492 (2010).
   PubMed Web of Science ®Google Scholar
• Becker D , SfakianakisI, KruppM et al. Genetic signatures shared in embryonic liver development and liver cancer define prognostically relevant subgroups in HCC. Mol. Cancer 11 , 55 (2012).
   PubMed Web of Science ®Google Scholar
• Farooq M , SulochanaKN, PanX et al. Histone deacetylase 3 (hdac3) is specifically required for liver development in zebrafish. Dev. Biol. 317(1) , 336–353 (2008).
   PubMed Web of Science ®Google Scholar
• Noel ES , Casal-SueiroA, Busch-NentwichE et al. Organ-specific requirements for Hdac1 in liver and pancreas formation. Dev. Biol. 322(2) , 237–250 (2008).
   PubMed Web of Science ®Google Scholar
• Lachenmayer A , ToffaninS, CabellosL et al. Combination therapy for hepatocellular carcinoma: additive preclinical efficacy of the HDAC inhibitor panobinostat with sorafenib. J. Hepatol. 56(6) , 1343–1350 (2012).
   PubMed Web of Science ®Google Scholar
• Quint K , AgaimyA, Di Fazio P et al. Clinical significance of histone deacetylases 1, 2, 3, and 7: HDAC2 is an independent predictor of survival in HCC. Virchows Arch.459(2) , 129–139 (2011).
   PubMed Web of Science ®Google Scholar
• Wu LM , YangZ, ZhouL et al. Identification of histone deacetylase 3 as a biomarker for tumor recurrence following liver transplantation in HBV-associated hepatocellular carcinoma. PLoS One 5(12) , e14460 (2010).
   PubMed Web of Science ®Google Scholar
• Zhang CZ , PanY, CaoY et al. Histone deacetylase inhibitors facilitate dihydroartemisinin-induced apoptosis in liver cancer in vitro and in vivo. PLoS One 7(6) , e39870 (2012).
   PubMed Web of Science ®Google Scholar
• Wong CW , PrivalskyML. Transcriptional repression by the SMRT–mSin3 corepressor: multiple interactions, multiple mechanisms, and a potential role for TFIIB. Mol. Cell Biol.18(9) , 5500–5510 (1998).
   PubMed Web of Science ®Google Scholar
• Karagianni P , WongJ. HDAC3: taking the SMRT-N-CoRrect road to repression. Oncogene26(37) , 5439–5449 (2007).
   PubMed Web of Science ®Google Scholar
• Ito T , ChibaT, OzawaR, YoshidaM, HattoriM, SakakiY. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA98(8) , 4569–4574 (2001).
   PubMed Web of Science ®Google Scholar
• Uetz P , GiotL, CagneyG et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403(6770) , 623–627 (2000).
   PubMed Web of Science ®Google Scholar
• Walhout AJ , SordellaR, LuX et al. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287(5450) , 116–122 (2000).
   PubMed Web of Science ®Google Scholar
• Gingras AC , GstaigerM, RaughtB, AebersoldR. Analysis of protein complexes using mass spectrometry. Nat. Rev. Mol. Cell Biol.8(8) , 645–654 (2007).
   PubMed Web of Science ®Google Scholar
• Kocher T , Superti-FurgaG. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods4(10) , 807–815 (2007).
   PubMed Web of Science ®Google Scholar
• Yin L , LazarMA. The orphan nuclear receptor Rev-erbα recruits the N-CoR/histone deacetylase 3 corepressor to regulate the circadian Bmal1 gene. Mol. Endocrinol.19(6) , 1452–1459 (2005).
   PubMedGoogle Scholar
• Farooq M , HozzeinWN, ElsayedEA, TahaNA, WadaanMA. Identification of histone deacetylase 1 protein complexes in liver cancer cells. Asian Pac. J. Cancer Prev.14(2) , 915–921 (2013).
   PubMedGoogle Scholar
• Glatter T , WepfA, AebersoldR, GstaigerM. An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol. Syst. Biol.5 , 237 (2009).
   PubMed Web of Science ®Google Scholar
• Olsen JV , SchwartzJC, Griep-RamingJ et al. A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol. Cell Proteomics 8(12) , 2759–2769 (2009).
   PubMed Web of Science ®Google Scholar
• Cowley MJ , PineseM, KassahnKS et al. PINA v2.0: mining interactome modules. Nucleic Acids Res. 40(Database issue) , D862–D865 (2012).
   PubMed Web of Science ®Google Scholar
• Ikenoue T , InokiK, ZhaoB, GuanKL. PTEN acetylation modulates its interaction with PDZ domain. Cancer Res.68(17) , 6908–6912 (2008).
   PubMed Web of Science ®Google Scholar
• de Ruijter AJ , van Gennip AH, Caron HN, Kemp S, van Kuilenburg AB. Histone deacetylases (HDACs): characterization of the classical HDAC family. Biochem. J.370(Pt 3) , 737–749 (2003).
   PubMed Web of Science ®Google Scholar
• Longworth MS , LaiminsLA. Histone deacetylase 3 localizes to the plasma membrane and is a substrate of Src. Oncogene25(32) , 4495–4500 (2006).
   PubMed Web of Science ®Google Scholar
• Lin HY , ChenCS, LinSP, WengJR. Targeting histone deacetylase in cancer therapy. Med. Res. Rev.26(4) , 397–413 (2006).
   PubMed Web of Science ®Google Scholar
• Delcuve GP , KhanDH, DavieJR. Targeting class I histone deacetylases in cancer therapy. Expert Opin. Ther. Targets17(1) , 29–41 (2013).
   PubMed Web of Science ®Google Scholar
• Gavin AC , AloyP, GrandiP et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440(7084) , 631–636 (2006).
   PubMed Web of Science ®Google Scholar
• Barret LA , PolidoriA, BonneteF, Bernard-SavaryP, JungasC. A new high-performance thin layer chromatography-based assay of detergents and surfactants commonly used in membrane protein studies. J. Chromatogr. A1281 , 135–141 (2013).
   PubMed Web of Science ®Google Scholar
• Bohm PS , SouthallJ, CogdellRJ, KohlerJ. Single-molecule spectroscopy on RC-LH1 complexes of Rhodopseudomonas acidophila strain 10.50.J. Phys. Chem. B117(11) , 3120–3126 (2013).
   PubMed Web of Science ®Google Scholar
• Yokota S , YamamotoY, ShimizuK et al. Increased expression of cytosolic chaperonin CCT in human hepatocellular and colonic carcinoma. Cell Stress Chaperones 6(4) , 345–350 (2001).
   PubMed Web of Science ®Google Scholar
• Guenther MG , BarakO, LazarMA. The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3. Mol. Cell Biol.21(18) , 6091–6101 (2001).
   PubMed Web of Science ®Google Scholar
• Wen YD , PerissiV, StaszewskiLM et al. The histone deacetylase-3 complex contains nuclear receptor corepressors. Proc. Natl Acad. Sci. USA 97(13) , 7202–7207 (2000).
   PubMed Web of Science ®Google Scholar
• Guenther MG , YuJ, KaoGD, YenTJ, LazarMA. Assembly of the SMRT-histone deacetylase 3 repression complex requires the TCP-1 ring complex. Genes Dev.16(24) , 3130–3135 (2002).
   PubMed Web of Science ®Google Scholar
• Tsuchiya H , IsedaT, HinoO. Identification of a novel protein (VBP-1) binding to the von Hippel–Lindau (VHL) tumor suppressor gene product. Cancer Res.56(13) , 2881–2885 (1996).
   PubMed Web of Science ®Google Scholar
• Brinke A , GreenPM, GiannelliF. Characterization of the gene (VBP1) and transcript for the von Hippel–Lindau binding protein and isolation of the highly conserved murine homologue. Genomics45(1) , 105–112 (1997).
   PubMed Web of Science ®Google Scholar
• Mori K , MaedaY, KitauraH, TairaT, Iguchi-ArigaSM, ArigaH. MM-1, a novel c-Myc-associating protein that represses transcriptional activity of c-Myc. J. Biol. Chem.273(45) , 29794–29800 (1998).
   PubMed Web of Science ®Google Scholar
• Vainberg IE , LewisSA, RommelaereH et al. Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin. Cell 93(5) , 863–873 (1998).
   PubMed Web of Science ®Google Scholar
• Fujioka Y , TairaT, MaedaY et al. MM-1, a c-Myc-binding protein, is a candidate for a tumor suppressor in leukemia/lymphoma and tongue cancer. J. Biol. Chem. 276(48) , 45137–45144 (2001).
   PubMed Web of Science ®Google Scholar
• Satou A , TairaT, Iguchi-ArigaSM, ArigaH. A novel transrepression pathway of c-Myc. Recruitment of a transcriptional corepressor complex to c-Myc by MM-1, a c-Myc-binding protein. J. Biol. Chem.276(49) , 46562–46567 (2001).
   PubMed Web of Science ®Google Scholar
• Guenther MG , LaneWS, FischleW, VerdinE, LazarMA, ShiekhattarR. A core SMRT corepressor complex containing HDAC3 and TBL1, a WD40-repeat protein linked to deafness. Genes Dev.14(9) , 1048–1057 (2000).
   PubMed Web of Science ®Google Scholar
• Yoon HG , ChoiY, ColePA, WongJ. Reading and function of a histone code involved in targeting corepressor complexes for repression. Mol. Cell Biol.25(1) , 324–335 (2005).
   PubMed Web of Science ®Google Scholar
• Kulozik P , JonesA, MattijssenF et al. Hepatic deficiency in transcriptional cofactor TBL1 promotes liver steatosis and hypertriglyceridemia. Cell Metab. 13(4) , 389–400 (2011).
   PubMed Web of Science ®Google Scholar
• Park EJ , LeeJH, YuGY et al. Dietary and genetic obesity promote liver inflammation and tumorigenesis by enhancing IL-6 and TNF expression. Cell 140(2) , 197–208 (2010).
   PubMed Web of Science ®Google Scholar
• Knutson SK , ChylaBJ, AmannJM, BhaskaraS, HuppertSS, HiebertSW. Liver-specific deletion of histone deacetylase 3 disrupts metabolic transcriptional networks. EMBO J.27(7) , 1017–1028 (2008).
   PubMed Web of Science ®Google Scholar
• Fleischer TC , YunUJ, AyerDE. Identification and characterization of three new components of the mSin3A corepressor complex. Mol. Cell Biol.23(10) , 3456–3467 (2003).
   PubMed Web of Science ®Google Scholar
• Lin YY , KiihlS, SuhailY et al. Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature 482(7384) , 251–255 (2012).
   PubMed Web of Science ®Google Scholar
• Yang WM , TsaiSC, WenYD, FejerG, SetoE. Functional domains of histone deacetylase-3. J. Biol. Chem.277(11) , 9447–9454 (2002).
   PubMed Web of Science ®Google Scholar
• Bantscheff M , HopfC, SavitskiMM et al. Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes. Nat. Biotechnol. 29(3) , 255–265 (2011).
   PubMed Web of Science ®Google Scholar
• Zhang J , KalkumM, ChaitBT, RoederRG. The N-CoR–HDAC3 nuclear receptor corepressor complex inhibits the JNK pathway through the integral subunit GPS2. Mol. Cell9(3) , 611–623 (2002).
   PubMed Web of Science ®Google Scholar
• Choi HK , ChoiKC, KangHB et al. Function of multiple Lis-Homology domain/WD-40 repeat-containing proteins in feed-forward transcriptional repression by silencing mediator for retinoic and thyroid receptor/nuclear receptor corepressor complexes. Mol. Endocrinol. 22(5) , 1093–1104 (2008).
   PubMedGoogle Scholar

Websites

• Biogrid. http://thebiogrid.org
   Google Scholar
• STRING. http://string-db.org
   Google Scholar
• Human Protein Atlas. www.proteinatlas.org
   Google Scholar
• Protein Interaction Network Analysis platform. http://cbg.garvan.unsw.edu.au/pina/home.do
   Google Scholar