Dose-responsive gene expression in suberoylanilide hydroxamic acid-treated resting CD4 + T cells

AIDS

Volumn 29, Issue 17, 2015, Pages 2235-2244

  Reardon, Brian ^a   Beliakova Bethell, Nadejda ^a   Spina, Celsa A ^b,c   Singhania, Akul ^d   Margolis, David M ^e   Richman, Douglas R ^a,b,c   Woelk, Christopher H ^d  

^a Department of Medicine ^*  (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

^d UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^e UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

dose response; histone deacetylase inhibitor; HIV; primary CD4 + T cells; suberoylanilide hydroxamic acid; transcriptome

Indexed keywords

BIOLOGICAL MARKER; CELL SURFACE MARKER; HISTONE METHYLTRANSFERASE; HUMAN IMMUNODEFICIENCY VIRUS PROTEIN; PROTEIN; TRANSCRIPTION FACTOR; VORINOSTAT; HISTONE DEACETYLASE INHIBITOR; HYDROXAMIC ACID;

ARTICLE; BINDING SITE; CD4+ T LYMPHOCYTE; CHROMATIN IMMUNOPRECIPITATION; DOSE RESPONSE; DOWN REGULATION; DRUG ACTIVITY; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE NUMBER; GENE ONTOLOGY; HISTONE ACETYLATION; HISTONE MODIFICATION; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS; IMMUNOMODULATION; IN VIVO STUDY; LATENT PERIOD; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; REAL TIME POLYMERASE CHAIN REACTION; T LYMPHOCYTE ACTIVATION; TREATMENT DURATION; UPREGULATION; VIRUS ACTIVATION; VIRUS CELL INTERACTION; VIRUS REPLICATION; CELL CULTURE; DRUG EFFECTS; GENE EXPRESSION PROFILING; TRANSCRIPTION INITIATION;

CD4-POSITIVE T-LYMPHOCYTES; CELLS, CULTURED; CHROMATIN IMMUNOPRECIPITATION; DOSE-RESPONSE RELATIONSHIP, DRUG; GENE EXPRESSION PROFILING; HISTONE DEACETYLASE INHIBITORS; HUMANS; HYDROXAMIC ACIDS; MICROARRAY ANALYSIS; TRANSCRIPTIONAL ACTIVATION;

EID: 84941348359     PISSN: 02699370     EISSN: 14735571     Source Type: Journal    
DOI: 10.1097/QAD.0000000000000839     Document Type: Article

References (46)

1. Lehrman G, Hogue IB, Palmer S, Jennings C, Spina CA, Wiegand A, et al. Depletion of latent HIV-1 infection in vivo: A proof-ofconcept study. Lancet 2005; 366:549-555.
2. Demonté D, Quivy V, Colette Y, Van Lint C. Administration of HDAC inhibitors to reactivate HIV-1 expression in latent cellular reservoirs: implications for the development of therapeutic strategies. Biochem Pharmacol 2004; 68:1231-1238.
3. Archin NM, Margolis DM. Emerging strategies to deplete the HIV reservoir. Curr Opin Infect Dis 2014; 27:29-35.
4. Mann BS, Johnson JR, Cohen MH, Justice R, Pazdur R. FDA approval summary: vorinostat for treatment of advanced primary cutaneous T-cell lymphoma. Oncologist 2007; 12:1247-1252.
5. Archin NM, Liberty AL, Kashuba AD, Choudhary SK, Kuruc JD, Crooks AM, et al. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature 2012; 487:482-485.
6. Archin NM, Bateson R, Tripathy MK, Crooks AM, Yang KH, Dahl NP, et al. HIV-1 expression within resting CD4R T cells after multiple doses of vorinostat. J Infect Dis 2014; 210:728-735.
7. Elliott JH, Wightman F, Solomon A, Ghneim K, Ahlers J, Cameron MJ, et al. Activation of HIV Transcription with Short-Course Vorinostat in HIV-Infected Patients on Suppressive Antiretroviral Therapy. PLoS Pathog 2014; 10:e1004473.
8. Rasmussen TA, Schmeltz Søgaard O, Brinkmann C, Wightman F, Lewin SR, Melchjorsen J, et al. Comparison of HDAC inhibitors in clinical development: Effect on HIV production in latently infected cells and T-cell activation. Hum Vaccin Immunother 2013; 9:.
9. Wei DG, Chiang V, Fyne E, Balakrishnan M, Barnes T, Graupe M, et al. Histone deacetylase inhibitor romidepsin induces HIV expression in CD4 T cells from patients on suppressive antiretroviral therapy at concentrations achieved by clinical dosing. PLoS Pathog 2014; 10:e1004071.
10. Matalon S, Rasmussen TA, Dinarello CA. Histone deacetylase inhibitors for purging HIV-1 from the latent reservoir. Mol Med 2011; 17:466-472.
11. Shirakawa K, Chavez L, Hakre S, Calvanese V, Verdin E. Reactivation of latent HIV by histone deacetylase inhibitors. Trends Microbiol 2013; 21:277-285.
12. Zain J, O'Connor OA. Targeting histone deacetyalses in the treatment of B-and T-cell malignancies. Invest New Drugs (28 Suppl 1):2010:S58-S78.
13. Beliakova-Bethell N, Zhang JX, Singhania A, Lee V, Terry VH, Richman DD, et al. Suberoylanilide hydroxamic acid induces limited changes in the transcriptome of primary CD4(R) T cells. AIDS 2013; 27:29-37.
14. Du P, Kibbe WA, Lin SM. lumi: A pipeline for processing Illumina microarray. Bioinformatics 2008; 24:1547-1548.
15. Pramana S, Lin D, Haldermans P, Shkedy Z, Verbeke T, Gohlmann H, et al. IsoGene: An R Package for Analyzing Doseresponse Studies in Microarray Experiments. R Journal 2010; 2:5-12.
16. Benjamini Y HY. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 1995; 57:289-300.
17. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 2003; 13:2498-2504.
18. Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009; 37:1-13.
19. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4:44-57.
20. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001; 25:402-408.
21. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 2013; 41:D64-69.
22. Gotea V, Ovcharenko I. DiRE: identifying distant regulatory elements of co-expressed genes. Nucleic Acids Res 2008; 36:W133-W139.
23. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 2003; 100:9440-9445.
24. Shan L, Deng K, Shroff NS, Durand CM, Rabi SA, Yang HC, et al. Stimulation of HIV-1-specific cytolytic T lymphocytes facilitates elimination of latent viral reservoir after virus reactivation. Immunity 2012; 36:491-501.
25. Sebastian S, Sreenivas P, Sambasivan R, Cheedipudi S, Kandalla P, Pavlath GK, et al. MLL5, a trithorax homolog, indirectly regulates H3K4 methylation, represses cyclin A2 expression, and promotes myogenic differentiation. Proc Natl Acad Sci U S A 2009; 106:4719-4724.
26. Lee JH, Tate CM, You JS, Skalnik DG. Identification and characterization of the human Set1B histone H3-Lys4 methyltransferase complex. J Biol Chem 2007; 282:13419-13428.
27. Tate CM, Lee JH, Skalnik DG. CXXC finger protein 1 restricts the Setd1A histone H3K4 methyltransferase complex to euchromatin. FEBS J 2010; 277:210-223.
28. Abu-Farha M, Lambert JP, Al-Madhoun AS, Elisma F, Skerjanc IS, Figeys D. The tale of two domains: proteomics and genomics analysis of SMYD2, a new histone methyltransferase. Mol Cell Proteomics 2008; 7:560-572.
29. Gu B, Lee MG. Histone H3 lysine 4 methyltransferases and demethylases in self-renewal and differentiation of stem cells. Cell Biosci 2013; 3:39.
30. Roh TY, Cuddapah S, Cui K, Zhao K. The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci U S A 2006; 103:15782-15787.
31. Daly K, Shirazi-Beechey SP. Microarray analysis of butyrate regulated genes in colonic epithelial cells. DNA Cell Biol 2006; 25:49-62.
32. Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, et al. Butyrate mediates decrease of histone acetylation centered on transcription start sites and downregulation of associated genes. Genome Res 2007; 17:708-719.
33. Peart MJ, Smyth GK, van Laar RK, Bowtell DD, Richon VM, Marks PA, et al. Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. Proc Natl Acad Sci U S A 2005; 102:3697-3702.
34. de Ruijter AJ, Meinsma RJ, Bosma P, Kemp S, Caron HN, van Kuilenburg AB. Gene expression profiling in response to the histone deacetylase inhibitor BL1521 in neuroblastoma. Exp Cell Res 2005; 309:451-467.
35. Grégoire IP, Richetta C, Meyniel-Schicklin L, Borel S, Pradezynski F, Diaz O, et al. IRGM is a common target of RNA viruses that subvert the autophagy network. PLoS Pathog 2011; 7:e1002422.
36. Agostini I, Popov S, Li J, Dubrovsky L, Hao T, Bukrinsky M. Heat-shock protein 70 can replace viral protein R of HIV-1 during nuclear import of the viral preintegration complex. Exp Cell Res 2000; 259:398-403.
37. Barr SD, Smiley JR, Bushman FD. The interferon response inhibits HIV particle production by induction of TRIM22. PLoS Pathog 2008; 4:e1000007.
38. Posada R, Pettoello-Mantovani M, Sieweke M, Graf T, Goldstein H. Suppression of HIV type 1 replication by a dominantnegative Ets-1 mutant. AIDS Res Hum Retroviruses 2000; 16:1981-1989.
39. Mukerjee R, Sawaya BE, Khalili K, Amini S. Association of p65 and C/EBPbeta with HIV-1 LTR modulates transcription of the viral promoter. J Cell Biochem 2007; 100:1210-1216.
40. Sheridan PL, Sheline CT, Cannon K, Voz ML, Pazin MJ, Kadonaga JT, et al. Activation of the HIV-1 enhancer by the LEF-1 HMG protein on nucleosome-assembled DNA in vitro. Genes Dev 1995; 9:2090-2104.
41. Shattock RJ, Rizzardi GP, Hayes P, Griffin GE. Engagement of adhesion molecules (CD18, CD11a, CD45, CD44, and CD58) enhances human immunodeficiency virus type 1 replication in monocytic cells through a tumor necrosis factor-modulated pathway. J Infect Dis 1996; 174:54-62.
42. Roscic-Mrkic B, Fischer M, Leemann C, Manrique A, Gordon CJ, Moore JP, et al. RANTES (CCL5) uses the proteoglycan CD44 as an auxiliary receptor to mediate cellular activation signals and HIV-1 enhancement. Blood 2003; 102:1169-1177.
43. He W, Neil S, Kulkarni H, Wright E, Agan BK, Marconi VC, et al. Duffy antigen receptor for chemokines mediates trans-infection of HIV-1 from red blood cells to target cells and affects HIV-AIDS susceptibility. Cell Host Microbe 2008; 4:52-62.
44. Ding D, Qu X, Li L, Zhou X, Liu S, Lin S, et al. Involvement of histone methyltransferase GLP in HIV-1 latency through catalysis of H3K9 dimethylation. Virology 2013; 440:182-189.
45. Bouchat S, Gatot JS, Kabeya K, Cardona C, Colin L, Herbein G, et al. Histone methyltransferase inhibitors induce HIV-1 recovery in resting CD4(R) T cells from HIV-1-infected HAARTtreated patients. AIDS 2012; 26:1473-1482.
46. Mohammadi P, di Iulio J, Munõz M, Martinez R, Bartha I, Cavassini M, et al. Dynamics of HIV latency and reactivation in a primary CD4R T cell model. PLoS Pathog 2014; 10: e1004156.