Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals

References

• Ay E, Banati F, Mezei M, Bakos A, Niller HH, Buzas K, Minarovits J. Epigenetics of HIV infection: promising research areas and implications for therapy. AIDS Rev 2013; 15(3):181-8; PMID:24002202
   PubMed Web of Science ®Google Scholar
• Paschos K, Allday MJ. Epigenetic reprogramming of host genes in viral and microbial pathogenesis. Trends Microbiol 2010; 18(10):439-47; PMID:20724161; http://dx.doi.org/10.1016/j.tim.2010.07.003
   PubMed Web of Science ®Google Scholar
• Harbers K, Schnieke A, Stuhlmann H, Jahner D, Jaenisch R. DNA methylation and gene expression: endogenous retroviral genome becomes infectious after molecular cloning. Proc Natl Acad Sci U S A 1981; 78(12):7609-13; PMID:6950402; http://dx.doi.org/10.1073/pnas.78.12.7609
   PubMed Web of Science ®Google Scholar
• Kumar A, Darcis G, Van Lint C, Herbein G. Epigenetic control of HIV-1 post integration latency: implications for therapy. Clin Epigenetics 2015; 7(1):103; PMID:26405463; http://dx.doi.org/10.1186/s13148-015-0137-6
   PubMed Web of Science ®Google Scholar
• Park J, Lim CH, Ham S, Kim SS, Choi BS, Roh TY. Genome-wide analysis of histone modifications in latently HIV-1 infected T cells. AIDS 2014; 28(12):1719-28; PMID:24762674; http://dx.doi.org/10.1097/QAD.0000000000000309
   PubMed Web of Science ®Google Scholar
• Bednarik DP, Cook JA, Pitha PM. Inactivation of the HIV LTR by DNA CpG methylation: evidence for a role in latency. EMBO J 1990; 9(4):1157-64; PMID:2323336
   PubMed Web of Science ®Google Scholar
• Kauder SE, Bosque A, Lindqvist A, Planelles V, Verdin E. Epigenetic regulation of HIV-1 latency by cytosine methylation. PLoS Pathog 2009; 5(6):e1000495; PMID:19557157; http://dx.doi.org/10.1371/journal.ppat.1000495
   PubMedGoogle Scholar
• Tripathy MK, Abbas W, Herbein G. Epigenetic regulation of HIV-1 transcription. Epigenomics 2011; 3(4):487-502; PMID:22126207; http://dx.doi.org/10.2217/epi.11.61
   PubMed Web of Science ®Google Scholar
• Blazkova J, Trejbalova K, Gondois-Rey F, Halfon P, Philibert P, Guiguen A, Verdin E, Olive D, Van Lint C, Hejnar J, et al. CpG methylation controls reactivation of HIV from latency. PLoS Pathog 2009; 5(8):e1000554; PMID:19696893; http://dx.doi.org/10.1371/journal.ppat.1000554
   PubMed Web of Science ®Google Scholar
• Deeks SG, Walker BD. Human immunodeficiency virus controllers: mechanisms of durable virus control in the absence of antiretroviral therapy. Immunity 2007; 27(3):406-16; PMID:17892849; http://dx.doi.org/10.1016/j.immuni.2007.08.010
   PubMed Web of Science ®Google Scholar
• Mikovits JA, Young HA, Vertino P, Issa JP, Pitha PM, Turcoski-Corrales S, Taub DD, Petrow CL, Baylin SB, Ruscetti FW. Infection with human immunodeficiency 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 1998; 18(9):5166-77; PMID:9710601; http://dx.doi.org/10.1128/MCB.18.9.5166
   PubMed Web of Science ®Google Scholar
• Fang JY, Mikovits JA, Bagni R, Petrow-Sadowski CL, Ruscetti FW. Infection of lymphoid cells by integration-defective human immunodeficiency virus type 1 increases de novo methylation. J Virol 2001; 75(20):9753-61; PMID:11559808; http://dx.doi.org/10.1128/JVI.75.20.9753-9761.2001
   PubMed Web of Science ®Google Scholar
• Pion M, Jaramillo-Ruiz D, Martinez A, Munoz-Fernandez MA, Correa-Rocha R. HIV infection of human regulatory T cells downregulates Foxp3 expression by increasing DNMT3b levels and DNA methylation in the FOXP3 gene. AIDS 2013; 27(13):2019-29; PMID:24201117; http://dx.doi.org/10.1097/QAD.0b013e32836253fd
   PubMed Web of Science ®Google Scholar
• Nakayama-Hosoya K, Ishida T, Youngblood B, Nakamura H, Hosoya N, Koga M, Koibuchi T, Iwamoto A, Kawana-Tachikawa A. Epigenetic repression of interleukin 2 expression in senescent CD4+ T cells during chronic HIV type 1 infection. J Infect Dis 2015; 211(1):28-39; PMID:25001463; http://dx.doi.org/10.1093/infdis/jiu376
   PubMed Web of Science ®Google Scholar
• Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, et al. Methylome-wide analysis of chronic HIV infection reveals five-year increase in biological age and epigenetic targeting of HLA. Mol Cell 2016; 62(2):157-68; PMID:27105112; http://dx.doi.org/10.1016/j.molcel.2016.03.019
   PubMed Web of Science ®Google Scholar
• De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, et al. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci 2014; 17(9):1156-63; PMID:25129075; http://dx.doi.org/10.1038/nn.3786
   PubMed Web of Science ®Google Scholar
• Liang L, Willis-Owen SA, Laprise C, Wong KC, Davies GA, Hudson TJ, Binia A, Hopkin JM, Yang IV, Grundberg E, et al. An epigenome-wide association study of total serum immunoglobulin E concentration. Nature 2015; 520(7549):670-4; PMID:25707804; http://dx.doi.org/10.1038/nature14125
   PubMed Web of Science ®Google Scholar
• Paul DS, Beck S. Advances in epigenome-wide association studies for common diseases. Trends Mol Med 2014; 20(10):541-3; PMID:25092140; http://dx.doi.org/10.1016/j.molmed.2014.07.002
   PubMed Web of Science ®Google Scholar
• Zhang Y, Li SK, Yi Yang K, Liu M, Lee N, Tang X, Wang H, Liu L, Chen Z, Zhang C, et al. Whole genome methylation array reveals the down-regulation of IGFBP6 and SATB2 by HIV-1. Sci Rep 2015; 5:10806; PMID:26039376; http://dx.doi.org/10.1038/srep10806
   PubMed Web of Science ®Google Scholar
• Lehne B, Drong AW, Loh M, Zhang W, Scott WR, Tan ST, Afzal U, Scott J, Jarvelin MR, Elliott P, et al. A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. Genome Biol 2015; 16:37; PMID:25853392; http://dx.doi.org/10.1186/s13059-015-0600-x
   PubMed Web of Science ®Google Scholar
• Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, Wiencke JK, Kelsey KT. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 2012; 13:86; PMID:22568884; http://dx.doi.org/10.1186/1471-2105-13-86
   PubMed Web of Science ®Google Scholar
• Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol 2014; 15(2):R31; PMID:24495553; http://dx.doi.org/10.1186/gb-2014-15-2-r31
   PubMed Web of Science ®Google Scholar
• Meissner TB, Li A, Biswas A, Lee KH, Liu YJ, Bayir E, Iliopoulos D, van den Elsen PJ, Kobayashi KS. NLR family member NLRC5 is a transcriptional regulator of MHC class I genes. Proc Natl Acad Sci U S A 2010; 107(31):13794-9; PMID:20639463; http://dx.doi.org/10.1073/pnas.1008684107
   PubMed Web of Science ®Google Scholar
• Anbanandam A, Albarado DC, Nguyen CT, Halder G, Gao X, Veeraraghavan S. Insights into transcription enhancer factor 1 (TEF-1) activity from the solution structure of the TEA domain. Proc Natl Acad Sci U S A 2006; 103(46):17225-30; PMID:17085591; http://dx.doi.org/10.1073/pnas.0607171103
   PubMed Web of Science ®Google Scholar
• Roth C, Schuierer M, Gunther K, Buettner R. Genomic structure and DNA binding properties of the human zinc finger transcriptional repressor AP-2rep (KLF12). Genomics 2000; 63(3):384-90; PMID:10704285; http://dx.doi.org/10.1006/geno.1999.6084
   PubMed Web of Science ®Google Scholar
• Hurlin PJ, Ayer DE, Grandori C, Eisenman RN. The Max transcription factor network: involvement of Mad in differentiation and an approach to identification of target genes. Cold Spring Harb Symp Quant Biol 1994; 59:109-16; PMID:7587059; http://dx.doi.org/10.1101/SQB.1994.059.01.014
   PubMedGoogle Scholar
• Klase Z, Yedavalli VS, Houzet L, Perkins M, Maldarelli F, Brenchley J, Strebel K, Liu P, Jeang KT. Activation of HIV-1 from latent infection via synergy of RUNX1 inhibitor Ro5-3335 and SAHA. PLoS Pathog 2014; 10(3):e1003997; PMID:24651404; http://dx.doi.org/10.1371/journal.ppat.1003997
   PubMedGoogle Scholar
• Landi A, Vermeire J, Iannucci V, Vanderstraeten H, Naessens E, Bentahir M, Verhasselt B. Genome-wide shRNA screening identifies host factors involved in early endocytic events for HIV-1-induced CD4 down-regulation. Retrovirology 2014; 11:118; PMID:25496667; http://dx.doi.org/10.1186/s12977-014-0118-4
   PubMed Web of Science ®Google Scholar
• Mehta S, Jeffrey KL. Beyond receptors and signaling: epigenetic factors in the regulation of innate immunity. Immunol Cell Biol 2015; 93(3):233-44; PMID:25559622; http://dx.doi.org/10.1038/icb.2014.101
   PubMed Web of Science ®Google Scholar
• Doerfler W. Beware of manipulations on the genome: epigenetic destabilization through (foreign) DNA insertions. Epigenomics 2016; 8(5):587-91; PMID:26997469; http://dx.doi.org/10.2217/epi-2016-0019
   PubMed Web of Science ®Google Scholar
• Doerfler W. Impact of foreign DNA integration on tumor biology and on evolution via epigenetic alterations. Epigenomics 2012; 4(1):41-9; PMID:22332657; http://dx.doi.org/10.2217/epi.11.111
   PubMed Web of Science ®Google Scholar
• Weber S, Hofmann A, Herms S, Hoffmann P, Doerfler W. Destabilization of the human epigenome: consequences of foreign DNA insertions. Epigenomics 2015; 7(5):745-55; PMID:26088384; http://dx.doi.org/10.2217/epi.15.40
   PubMed Web of Science ®Google Scholar
• Kobayashi KS, van den Elsen PJ. NLRC5: a key regulator of MHC class I-dependent immune responses. Nat Rev Immunol 2012; 12(12):813-820; PMID:23175229; http://dx.doi.org/10.1038/nri3339
   PubMed Web of Science ®Google Scholar
• Lamkanfi M, Kanneganti TD. Regulation of immune pathways by the NOD-like receptor NLRC5. Immunobiology 2012; 217(1):13-6; PMID:22024701; http://dx.doi.org/10.1016/j.imbio.2011.08.011
   PubMed Web of Science ®Google Scholar
• Yao Y, Wang Y, Chen F, Huang Y, Zhu S, Leng Q, Wang H, Shi Y, Qian Y. NLRC5 regulates MHC class I antigen presentation in host defense against intracellular pathogens. Cell Res 2012; 22(5):836-47; PMID:22491475; http://dx.doi.org/10.1038/cr.2012.56
   PubMed Web of Science ®Google Scholar
• Staehli F, Ludigs K, Heinz LX, Seguin-Estevez Q, Ferrero I, Braun M, Schroder K, Rebsamen M, Tardivel A, Mattmann C, et al. NLRC5 deficiency selectively impairs MHC class I- dependent lymphocyte killing by cytotoxic T cells. J Immunol 2012; 188(8):3820-8; PMID:22412192; http://dx.doi.org/10.4049/jimmunol.1102671
   PubMed Web of Science ®Google Scholar
• Neerincx A, Rodriguez GM, Steimle V, Kufer TA. NLRC5 controls basal MHC class I gene expression in an MHC enhanceosome-dependent manner. J Immunol 2012; 188(10):4940-50; PMID:22490867; http://dx.doi.org/10.4049/jimmunol.1103136
   PubMed Web of Science ®Google Scholar
• Biswas A, Meissner TB, Kawai T, Kobayashi KS. Cutting edge: impaired MHC class I expression in mice deficient for Nlrc5/class I transactivator. J Immunol 2012; 189(2):516-20; PMID:22711889; http://dx.doi.org/10.4049/jimmunol.1200064
   PubMed Web of Science ®Google Scholar
• Meissner TB, Liu YJ, Lee KH, Li A, Biswas A, van Eggermond MC, van den Elsen PJ, Kobayashi KS. NLRC5 cooperates with the RFX transcription factor complex to induce MHC class I gene expression. J Immunol 2012; 188(10):4951-8; PMID:22490869; http://dx.doi.org/10.4049/jimmunol.1103160
   PubMed Web of Science ®Google Scholar
• Yoshihama S, Roszik J, Downs I, Meissner TB, Vijayan S, Chapuy B, Sidiq T, Shipp MA, Lizee GA, Kobayashi KS. NLRC5/MHC class I transactivator is a target for immune evasion in cancer. Proc Natl Acad Sci U S A 2016; 113(21):5999-6004; PMID:27162338; http://dx.doi.org/10.1073/pnas.1602069113
   PubMed Web of Science ®Google Scholar
• Cui J, Zhu L, Xia X, Wang HY, Legras X, Hong J, Ji J, Shen P, Zheng S, Chen ZJ, et al. NLRC5 negatively regulates the NF-kappaB and type I interferon signaling pathways. Cell 2010; 141(3):483-96; PMID:20434986; http://dx.doi.org/10.1016/j.cell.2010.03.040
   PubMed Web of Science ®Google Scholar
• Tong Y, Cui J, Li Q, Zou J, Wang HY, Wang RF. Enhanced TLR-induced NF-kappaB signaling and type I interferon responses in NLRC5 deficient mice. Cell Res 2012; 22(5):822-35; PMID:22473004; http://dx.doi.org/10.1038/cr.2012.53
   PubMed Web of Science ®Google Scholar
• Soupene E, Kuypers FA. Phosphatidylcholine formation by LPCAT1 is regulated by Ca(2+) and the redox status of the cell. BMC Biochem 2012; 13:8; PMID:22676268; http://dx.doi.org/10.1186/1471-2091-13-8
   PubMed Web of Science ®Google Scholar
• Harayama T, Shindou H, Ogasawara R, Suwabe A, Shimizu T. Identification of a novel noninflammatory biosynthetic pathway of platelet-activating factor. J Biol Chem 2008; 283(17):11097-106; PMID:18285344; http://dx.doi.org/10.1074/jbc.M708909200
   PubMed Web of Science ®Google Scholar
• Verma M. Epigenetic regulation of HIV, AIDS, and AIDS-related malignancies. Methods Mol Biol 2015; 1238:381-403; PMID:25421672; http://dx.doi.org/10.1007/978-1-4939-1804-1_21
   PubMedGoogle Scholar
• Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, Runarsson A, Reinius L, Acevedo N, Taub M, Ronninger M, et al. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol 2013; 31(2):142-7; PMID:23334450; http://dx.doi.org/10.1038/nbt.2487
   PubMed Web of Science ®Google Scholar
• Langevin SM, Houseman EA, Accomando WP, Koestler DC, Christensen BC, Nelson HH, Karagas MR, Marsit CJ, Wiencke JK, Kelsey KT. Leukocyte-adjusted epigenome-wide association studies of blood from solid tumor patients. Epigenetics 2014; 9(6):884-95; PMID:24671036; http://dx.doi.org/10.4161/epi.28575
   PubMed Web of Science ®Google Scholar
• Nelson G, Jia L, Elloumi F, Binns E, Goedert JJ, Limou S, Winkler C. Adjusting infinium methylation profiles to suppress signals from varying cell proportion. Am Soc Hum Genet 2015; PMID:26404086
   PubMedGoogle Scholar
• Fultz SL, Skanderson M, Mole LA, Gandhi N, Bryant K, Crystal S, Justice AC. Development and verification of a “virtual” cohort using the National VA Health Information System. Med Care 2006; 44(8 Suppl 2):S25-30; PMID:16849965; http://dx.doi.org/10.1097/01.mlr.0000223670.00890.74
   PubMed Web of Science ®Google Scholar
• Horvath S, Levine AJ. HIV-1 infection accelerates age according to the epigenetic clock. J Infect Dis 2015; 212(10):1563-73; PMID:25969563; http://dx.doi.org/10.1093/infdis/jiv277
   PubMed Web of Science ®Google Scholar
• Reynolds LM, Taylor JR, Ding J, Lohman K, Johnson C, Siscovick D, Burke G, Post W, Shea S, Jacobs DR, Jr, et al. Age-related variations in the methylome associated with gene expression in human monocytes and T cells. Nat Commun 2014; 5:5366; PMID:25404168; http://dx.doi.org/10.1038/ncomms6366
   PubMed Web of Science ®Google Scholar
• Bacalini MG, Boattini A, Gentilini D, Giampieri E, Pirazzini C, Giuliani C, Fontanesi E, Remondini D, Capri M, Del Rio A, et al. A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data. Aging (Albany NY) 2015; 7(2):97-109; PMID:25701668; http://dx.doi.org/10.18632/aging.100718
   PubMedGoogle Scholar
• Garagnani P, Bacalini MG, Pirazzini C, Gori D, Giuliani C, Mari D, Di Blasio AM, Gentilini D, Vitale G, Collino S, et al. Methylation of ELOVL2 gene as a new epigenetic marker of age. Aging Cell 2012; 11(6):1132-4; PMID:23061750; http://dx.doi.org/10.1111/acel.12005
   PubMed Web of Science ®Google Scholar
• Bekaert B, Kamalandua A, Zapico SC, Van de Voorde W, Decorte R. Improved age determination of blood and teeth samples using a selected set of DNA methylation markers. Epigenetics 2015; 10(10):922-30; PMID:26280308; http://dx.doi.org/10.1080/15592294.2015.1080413
   PubMed Web of Science ®Google Scholar