HIV-induced epigenetic alterations in host cells

Advances in Experimental Medicine and Biology

Volumn 879, Issue , 2016, Pages 27-38

  Abdel Hameed, Enass A ^a   Ji, Hong ^b   Shata, Mohamed Tarek ^a  

^a UNIVERSITY OF CINCINNATI MEDICAL CENTER   (United States)

^b CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

Author keywords

De novo methylation; Histone deacetylase inhibitors; HIV latency; T cell specifi c genes; Shock and kill therapy

Indexed keywords

AZACITIDINE; CHEMOKINE RECEPTOR CCR5; DECITABINE; DNA METHYLTRANSFERASE; DNA METHYLTRANSFERASE 1; ELLAGIC ACID; HISTONE DEACETYLASE; HISTONE DEMETHYLASE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; LONG UNTRANSLATED RNA; METHYL CPG BINDING PROTEIN 2; NEF PROTEIN; POLYCOMB REPRESSIVE COMPLEX 2; PROTEIN P50; PROTEIN S 100; QUINAZOLINE DERIVATIVE; ROMIDEPSIN; SINGLE STRANDED DNA; TRANSACTIVATOR PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR EZH2; TRANSCRIPTION FACTOR FOXP3; TRANSCRIPTION FACTOR YY1; VALPROIC ACID; VORINOSTAT; VPR PROTEIN;

ADAPTIVE IMMUNITY; CELL DIFFERENTIATION; CPG ISLAND; DISEASE COURSE; DNA METHYLATION; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; GENE MUTATION; GENETIC TRANSCRIPTION; HISTONE MODIFICATION; HOST CELL; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE RESPONSE; LONG TERMINAL REPEAT; MONONUCLEAR CELL; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; PROTEIN PROCESSING; PROTEIN TARGETING; UPREGULATION; VIRUS DNA CELL DNA INTERACTION; VIRUS GENE; VIRUS LATENCY; VIRUS REACTIVATION; VIRUS REPLICATION; ANIMAL; CD4+ T LYMPHOCYTE; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; METABOLISM; PHYSIOLOGY; VIROLOGY; VIRUS GENOME;

ANIMALS; CD4-POSITIVE T-LYMPHOCYTES; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, VIRAL; GENOME, VIRAL; HIV INFECTIONS; HIV-1; HIV-2; HUMANS; VIRUS LATENCY;

EID: 84949650490     PISSN: 00652598     EISSN: 22148019     Source Type: Book Series    
DOI: 10.1007/978-3-319-24738-0_2     Document Type: Chapter

References (71)

1. Abdel-Hameed EA, Ji H, Sherman KE, Shata MT (2014) Epigenetic modifi cation of FOXP3 in patients with chronic HIV infection. J Acquir Immune Defi c Syndr 65:19-26
2. Atianand MK, Fitzgerald KA (2014) Long non-coding RNAs and control of gene expression in the immune system. Trends Mol Med 20:623-631
3. Baltimore D, Boldin MP, O’Connell RM, Rao DS, Taganov KD (2008) MicroRNAs: new regulators of immune cell development and function. Nat Immunol 9:839-845
4. Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A (2009) An operational defi nition of epigenetics. Genes Dev 23:781-783
5. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315-326
6. Bignami F, Pilotti E, Bertoncelli L, Ronzi P, Gulli M, Marmiroli N, Magnani G, Pinti M, Lopalco L, Mussini C, Ruotolo R, Galli M, Cossarizza A, Casoli C (2012) Stable changes in CD4+ T lymphocyte miRNA expression after exposure to HIV-1. Blood 119:6259-6267
7. Blazkova J, Trejbalova K, Gondois-Rey F, Halfon P, Philibert P, Guiguen A, Verdin E, Olive D, Van Lint C, Hejnar J, Hirsch I (2009) CpG methylation controls reactivation of HIV from latency. PLoS Pathog 5:e1000554
8. Bohnlein E, Lowenthal JW, Siekevitz M, Ballard DW, Franza BR, Greene WC (1988) The same inducible nuclear proteins regulates mitogen activation of both the interleukin-2 receptor-alpha gene and type 1 HIV. Cell 53:827-836
9. Boland MJ, Nazor KL, Loring JF (2014) Epigenetic regulation of pluripotency and differentiation. Circ Res 115:311-324
10. Britton LM, Sova P, Belisle S, Liu S, Chan EY, Katze MG, Garcia BA (2014) A proteomic glimpse into the initial global epigenetic changes during HIV infection. Proteomics 14:2226-2230
11. Burnett JC, Rossi JJ (2012) RNA-based therapeutics: current progress and future prospects. Chem Biol 19:60-71
12. Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C (2005) Genome-wide analysis of retroviral DNA integration. Nat Rev Microbiol 3:848-858
13. Chen BK, Feinberg MB, Baltimore D (1997) The kappaB sites in the human immunodefi ciency virus type 1 long terminal repeat enhance virus replication yet are not absolutely required for viral growth. J Virol 71:5495-5504
14. Chene L, Nugeyre MT, Barre-Sinoussi F, Israel N (1999) High-level replication of human immunodefi ciency virus in thymocytes requires NF-kappaB activation through interaction with thymic epithelial cells. J Virol 73:2064-2073
15. Christman JK (2002) 5-Azacytidine and 5-aza-2′-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy. Oncogene 21:5483-5495
16. Colin L, Van Lint C (2009) Molecular control of HIV-1 postintegration latency: implications for the development of new therapeutic strategies. Retrovirology 6:111
17. Coull JJ, Romerio F, Sun JM, Volker JL, Galvin KM, Davie JR, Shi Y, Hansen U, Margolis DM (2000) The human factors YY1 and LSF repress the human immunodefi ciency virus type 1 long terminal repeat via recruitment of histone deacetylase 1. J Virol 74:6790-6799
18. Cullen SM, Mayle A, Rossi L, Goodell MA (2014) Hematopoietic stem cell development: an epigenetic journey. Curr Top Dev Biol 107:39-75
19. Dollard SC, Gummuluru S, Tsang S, Fultz PN, Dewhurst S (1994) Enhanced responsiveness to nuclear factor kappa B contributes to the unique phenotype of simian immunodefi ciency virus variant SIVsmmPBj14. J Virol 68:7800-7809
20. Duverger A, Jones J, May J, Bibollet-Ruche F, Wagner FA, Cron RQ, Kutsch O (2009) Determinants of the establishment of human immunodefi ciency virus type 1 latency. J Virol 83:3078-3093
21. Easley R, Van Duyne R, Coley W, Guendel I, Dadgar S, Kehn-Hall K, Kashanchi F (2010) Chromatin dynamics associated with HIV-1 Tat-activated transcription. Biochim Biophys Acta 1799:275-285
22. Engelman A, Mizuuchi K, Craigie R (1991) HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell 67:1211-1221
23. Engelman A, Kessl JJ, Kvaratskhelia M (2013) Allosteric inhibition of HIV-1 integrase activity. Curr Opin Chem Biol 17:339-345
24. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE (2011) Mapping and analysis of chromatin state dynamics innine human cell types. Nature 473:43-49
25. Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 107:8689-8694
26. Fowler L, Saksena NK (2013) Micro-RNA: new players in HIV-pathogenesis, diagnosis, prognosis and antiviral therapy. AIDS Rev 15:3-14
27. Friedman J, Cho WK, Chu CK, Keedy KS, Archin NM, Margolis DM, Karn J (2011) Epigenetic silencing of HIV-1 by the histone H3 lysine 27 methyltransferase enhancer of Zeste 2. J Virol 85:9078-9089
28. Ganesh L, Burstein E, Guha-Niyogi A, Louder MK, Mascola JR, Klomp LW, Wijmenga C, Duckett CS, Nabel GJ (2003) The gene product Murr1 restricts HIV-1 replication in resting CD4+ lymphocytes. Nature 426:853-857
29. Gilmore TD (2006) Introduction to NF-kappaB: players, pathways, perspectives. Oncogene 25:6680-6684
30. Giordanengo V, Ollier L, Lanteri M, Lesimple J, March D, Thyss S, Lefebvre JC (2004) Epigenetic reprogramming of UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) in HIV-1-infected CEM T cells. FASEB J 18:1961-1963
31. Grant C, Oh U, Fugo K, Takenouchi N, Griffi th C, Yao K, Newhook TE, Ratner L, Jacobson S (2006) Foxp3 represses retroviral transcription by targeting both NF-kappaB and CREB pathways. PLoS Pathog 2:e33
32. Guttman M, Rinn JL (2012) Modular regulatory principles of large non-coding RNAs. Nature 482:339-346
33. Hill PW, Amouroux R, Hajkova P (2014) DNA demethylation, Tet proteins and 5-hydroxymethylcytosine in epigenetic reprogramming: an emerging complex story. Genomics 104:324-333
34. Huang J, Wang F, Argyris E, Chen K, Liang Z, Tian H, Huang W, Squires K, Verlinghieri G, Zhang H (2007) Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med 13:1241-1247
35. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissuespecifi c CpG island shores. Nat Genet 41:178-186
36. Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P, Lee H, Aryee MJ, Irizarry RA, Kim K, Rossi DJ, Inlay MA, Serwold T, Karsunky H, Ho L, Daley GQ, Weissman IL, Feinberg AP (2010) Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 467:338-342
37. Jones KA, Peterlin BM (1994) Control of RNA initiation and elongation at the HIV-1 promoter. Annu Rev Biochem 63:717-743
38. Kauder SE, Bosque A, Lindqvist A, Planelles V, Verdin E (2009) Epigenetic regulation of HIV-1 latency by cytosine methylation. PLoS Pathog 5:e1000495
39. Kinoshita S, Su L, Amano M, Timmerman LA, Kaneshima H, Nolan GP (1997) The T cell activation factor NF-ATc positively regulates HIV-1 replication and gene expression in T cells. Immunity 6:235-244
40. Klase Z, Houzet L, Jeang KT (2012) MicroRNAs and HIV-1: complex interactions. J Biol Chem 287:40884-40890
41. Klose RJ, Bird AP (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31:89-97
42. Lassen K, Han Y, Zhou Y, Siliciano J, Siliciano RF (2004) The multifactorial nature of HIV-1 latency. Trends Mol Med 10:525-531
43. Leonard J, Parrott C, Buckler-White AJ, Turner W, Ross EK, Martin MA, Rabson AB (1989) The NF-kappa B binding sites in the human immunodefi ciency virus type 1 long terminal repeat are not required for virus infectivity. J Virol 63:4919-4924
44. Mikovits JA, Young HA, Vertino P, Issa JP, Pitha PM, Turcoski-Corrales S, Taub DD, Petrow CL, Baylin SB, Ruscetti FW (1998) Infection with human immunodefi ciency virus type 1 upregulates DNA methyltransferase, resulting in de novo methylation of the gamma interferon (IFN-gamma) promoter and subsequent downregulation of IFN-gamma production. Mol Cell Biol 18:5166-5177
45. Nabel G, Baltimore D (1987) An inducible transcription factor activates expression of human immunodefi -ciency virus in T cells. Nature 326:711-713
46. Palacios JA, Perez-Pinar T, Toro C, Sanz-Minguela B, Moreno V, Valencia E, Gomez-Hernando C, Rodes B (2012) Long-term nonprogressor and elite controller patients who control viremia have a higher percentage of methylation in their HIV-1 proviral promoters than aviremic patients receiving highly active antiretroviral therapy. J Virol 86:13081-13084
47. Pion M, Jaramillo-Ruiz D, Martinez A, Munoz-Fernandez MA, Correa-Rocha R (2013) HIV infection of human regulatory T cells downregulates Foxp3 expression by increasing DNMT3b levels and DNA methylation in the FOXP3 gene. AIDS 27:2019-2029
48. Poveda E (2014) Ingenol derivates promising for HIV eradication. AIDS Rev 16:246
49. Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145-166
50. Saayman S, Ackley A, Turner AM, Famiglietti M, Bosque A, Clemson M, Planelles V, Morris KV (2014) An HIVencoded antisense long noncoding RNA epigenetically regulates viral transcription. Mol Ther 22:1164-1175
51. Selby MJ, Peterlin BM (1990) Trans-activation by HIV-1 Tat via a heterologous RNA binding protein. Cell 62:769-776
52. Serrao E, Krishnan L, Shun MC, Li X, Cherepanov P, Engelman A, Maertens GN (2014) Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: implications for the mechanism of target DNA binding. Nucleic Acids Res 42:5164-5176
53. Shan L, Yang HC, Rabi SA, Bravo HC, Shroff NS, Irizarry RA, Zhang H, Margolick JB, Siliciano JD, Siliciano RF (2011) Infl uence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model. J Virol 85:5384-5393
54. Sun G, Li H, Wu X, Covarrubias M, Scherer L, Meinking K, Luk B, Chomchan P, Alluin J, Gombart AF, Rossi JJ (2012) Interplay between HIV-1 infection and host microRNAs. Nucleic Acids Res 40:2181-2196
55. Swaminathan G, Navas-Martin S, Martin-Garcia J (2014) MicroRNAs and HIV-1 infection: antiviral activities and beyond. J Mol Biol 426:1178-1197
56. Tan Gana NH, Onuki T, Victoriano AF, Okamoto T (2012) MicroRNAs in HIV-1 infection: an integration of viral and cellular interaction at the genomic level. Front Microbiol 3:306
57. Timp W, Feinberg AP (2013) Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer 13:497-510
58. Tyagi M, Pearson RJ, Karn J (2010) Establishment of HIV latency in primary CD4+ cells is due to epigenetic transcriptional silencing and P-TEFb restriction. J Virol 84:6425-6437
59. Van Lint C, Bouchat S, Marcello A (2013) HIV-1 transcription and latency: an update. Retrovirology 10:67
60. Waddington CH (1953) Epigenetics and evolution. Symp Soc Exp Biol 7:186-199
61. Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD(2007) HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifi cations. Genome Res 17:1186-1194
62. Wang P, Xue Y, Han Y, Lin L, Wu C, Xu S, Jiang Z, Xu J, Liu Q, Cao X (2014) The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science 344:310-313
63. Wei DG, Chiang V, Fyne E, Balakrishnan M, Barnes T, Graupe M, Hesselgesser J, Irrinki A, Murry JP, Stepan G, Stray KM, Tsai A, Yu H, Spindler J, Kearney M, Spina CA, McMahon D, Lalezari J, Sloan D, Mellors J, Geleziunas R, Cihlar T (2014) 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 10:e1004071
64. West MJ, Lowe AD, Karn J (2001) Activation of human immunodefi ciency virus transcription in T cells revisited: NF-kappaB p65 stimulates transcriptional elongation. J Virol 75:8524-8537
65. Williams SA, Greene WC (2007) Regulation of HIV-1 latency by T-cell activation. Cytokine 39:63-74
66. Williams SA, Chen LF, Kwon H, Ruiz-Jarabo CM, Verdin E, Greene WC (2006) NF-kappaB p50 promotes HIV latency through HDAC recruitment and repression of transcriptional initiation. EMBO J 25:139-149
67. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG (2005) A strategy for probing the function of noncoding RNAs fi nds a repressor of NFAT. Science 309:1570-1573
68. Youngblood B, Reich NO (2008) The early expressed HIV-1 genes regulate DNMT1 expression. Epigenetics 3:149-156
69. Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916-919
70. Zhang X, Ulm A, Somineni HK, Oh S, Weirauch MT, Zhang HX, Chen X, Lehn MA, Janssen EM, Ji H (2014) DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells. Epigenetics Chromatin 7:21
71. Zhu J, Yamane H, Paul WE (2010) Differentiation of effector CD4 T cell populations. Annu Rev Immunol 28:445-489