{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T02:25:52Z","timestamp":1785205552222,"version":"3.55.0"},"reference-count":51,"publisher":"Elsevier BV","issue":"5","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,7,6]],"date-time":"2025-07-06T00:00:00Z","timestamp":1751760000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People's Republic of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFC2305002"],"award-info":[{"award-number":["2022YFC2305002"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Genomics"],"published-print":{"date-parts":[[2025,9]]},"DOI":"10.1016\/j.ygeno.2025.111082","type":"journal-article","created":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T15:26:14Z","timestamp":1752593174000},"page":"111082","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["Global transcriptome characterization of peripheral blood mononuclear cells in individuals with chronic HIV infection"],"prefix":"10.1016","volume":"117","author":[{"given":"Han-Ying","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian-Qian","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xing-Zhong","family":"Miao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang-Juan","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Jun","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong-Bo","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ygeno.2025.111082_bb0005","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/S0140-6736(23)01381-8","article-title":"HIV epidemiology, prevention, treatment, and implementation strategies for public health","volume":"403","author":"Mody","year":"2024","journal-title":"Lancet (London, England)"},{"key":"10.1016\/j.ygeno.2025.111082_bb0010","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/S0140-6736(23)00877-2","article-title":"The risk of sexual transmission of HIV in individuals with low-level HIV viraemia: a systematic review","volume":"402","author":"Broyles","year":"2023","journal-title":"Lancet (London, England)"},{"key":"10.1016\/j.ygeno.2025.111082_bb0015","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1056\/NEJMoa1506816","article-title":"Initiation of antiretroviral therapy in early asymptomatic HIV infection","volume":"373","author":"Lundgren","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ygeno.2025.111082_bb0020","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1056\/NEJMcp1915826","article-title":"HIV infection - screening, diagnosis, and treatment","volume":"384","author":"Saag","year":"2021","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ygeno.2025.111082_bb0025","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1038\/s41572-023-00452-3","article-title":"HIV infection","volume":"9","author":"Bekker","year":"2023","journal-title":"Nat. Rev. Dis. Prim."},{"key":"10.1016\/j.ygeno.2025.111082_bb0030","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1002\/JLB.4MR1019-189R","article-title":"Incomplete immune reconstitution in HIV\/AIDS patients on antiretroviral therapy: challenges of immunological non-responders","volume":"107","author":"Yang","year":"2020","journal-title":"J. Leukoc. Biol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0035","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.it.2010.12.002","article-title":"Immune reconstitution after a decade of combined antiretroviral therapies for human immunodeficiency virus","volume":"32","author":"Guihot","year":"2011","journal-title":"Trends Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0040","article-title":"Adjunct therapy for CD4(+) T-cell recovery, inflammation and immune activation in people living with HIV: a systematic review and Meta-analysis","volume":"12","author":"Zhang","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0045","doi-asserted-by":"crossref","first-page":"1228795","DOI":"10.3389\/fimmu.2023.1228795","article-title":"Multi-omics in HIV: searching insights to understand immunological non-response in PLHIV","volume":"14","author":"Espineira","year":"2023","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0050","first-page":"155","article-title":"Failure of CD4+ T-cell recovery upon virally-effective cART: an enduring gap in the understanding of HIV+ immunological non-responders","volume":"45","author":"Bono","year":"2022","journal-title":"New Microbiol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0055","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41586-020-2651-8","article-title":"Distinct viral reservoirs in individuals with spontaneous control of HIV-1","volume":"585","author":"Jiang","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2025.111082_bb0060","doi-asserted-by":"crossref","first-page":"135","DOI":"10.7326\/M21-4336","article-title":"The Esperanza patient: more Hope for a sterilizing HIV-1 cure","volume":"175","author":"Blankson","year":"2022","journal-title":"Ann. Intern. Med."},{"key":"10.1016\/j.ygeno.2025.111082_bb0065","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01805-17","article-title":"Factors leading to the loss of natural elite control of HIV-1 infection","volume":"92","author":"Pernas","year":"2018","journal-title":"J. Virol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0070","doi-asserted-by":"crossref","first-page":"2085","DOI":"10.1038\/s41591-021-01590-5","article-title":"Research priorities for an HIV cure: international AIDS society global scientific strategy 2021","volume":"27","author":"Deeks","year":"2021","journal-title":"Nat. Med."},{"key":"10.1016\/j.ygeno.2025.111082_bb0075","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1126\/science.369.6507.1045","article-title":"How \u2018elite Controllers\u2019 Tame HIV without Drugs","volume":"avol. 369","author":"Cohen","year":"2020","journal-title":"Science (New York, N.Y.)"},{"key":"10.1016\/j.ygeno.2025.111082_bb0080","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/nri.2017.99","article-title":"The spectrum of T cell metabolism in health and disease","volume":"18","author":"Bantug","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0085","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/s41577-020-0381-7","article-title":"Immunometabolism and HIV-1 pathogenesis: food for thought","volume":"21","author":"S\u00e1ez-Ciri\u00f3n","year":"2021","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0090","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/s41590-021-00898-1","article-title":"Multi-omics analyses reveal that HIV-1 alters CD4(+) T cell immunometabolism to fuel virus replication","volume":"22","author":"Guo","year":"2021","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0095","article-title":"Editorial: T cell metabolism in infection","volume":"13","author":"Xu","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0100","doi-asserted-by":"crossref","first-page":"5956","DOI":"10.1038\/s41467-022-33401-x","article-title":"S100A8-mediated metabolic adaptation controls HIV-1 persistence in macrophages in vivo","volume":"13","author":"Real","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ygeno.2025.111082_bb0105","doi-asserted-by":"crossref","DOI":"10.15252\/emmm.202013901","article-title":"Glycolysis downregulation is a hallmark of HIV-1 latency and sensitizes infected cells to oxidative stress","volume":"13","author":"Shytaj","year":"2021","journal-title":"EMBO Mol. Med."},{"key":"10.1016\/j.ygeno.2025.111082_bb0110","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1038\/s41421-021-00367-x","article-title":"Global transcriptomic characterization of T cells in individuals with chronic HIV-1 infection","volume":"8","author":"Wang","year":"2022","journal-title":"Cell discovery"},{"key":"10.1016\/j.ygeno.2025.111082_bb0115","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1038\/nm.4023","article-title":"Killer lymphocytes use granulysin, perforin and granzymes to kill intracellular parasites","volume":"22","author":"Dotiwala","year":"2016","journal-title":"Nat. Med."},{"key":"10.1016\/j.ygeno.2025.111082_bb0120","doi-asserted-by":"crossref","first-page":"1254155","DOI":"10.3389\/fimmu.2023.1254155","article-title":"Altered plasma metabolites and inflammatory networks in HIV-1 infected patients with different immunological responses after long-term antiretroviral therapy","volume":"14","author":"Lu","year":"2023","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0125","doi-asserted-by":"crossref","first-page":"7874","DOI":"10.1128\/JVI.76.15.7874-7882.2002","article-title":"Pharmacological cyclin-dependent kinase inhibitors inhibit replication of wild-type and drug-resistant strains of herpes simplex virus and human immunodeficiency virus type 1 by targeting cellular, not viral, proteins","volume":"76","author":"Schang","year":"2002","journal-title":"J. Virol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0130","doi-asserted-by":"crossref","first-page":"4785","DOI":"10.1111\/bph.13257","article-title":"Phosphodiesterase 4D: an enzyme to remember","volume":"172","author":"Ricciarelli","year":"2015","journal-title":"Br. J. Pharmacol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0135","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/nbt.1598","article-title":"Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety","volume":"28","author":"Burgin","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0140","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1124\/pr.110.003707","article-title":"Exchange protein directly activated by cAMP (epac): a multidomain cAMP mediator in the regulation of diverse biological functions","volume":"65","author":"Schmidt","year":"2013","journal-title":"Pharmacol. Rev."},{"key":"10.1016\/j.ygeno.2025.111082_bb0145","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1128\/CMR.00015-16","article-title":"Total HIV-1 DNA, a marker of viral reservoir dynamics with clinical implications","volume":"29","author":"Avettand-F\u00e8no\u00ebl","year":"2016","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.ygeno.2025.111082_bb0150","first-page":"22","article-title":"Celastrol mitigates inflammation in sepsis by inhibiting the PKM2-dependent Warburg effect","volume":"9","author":"Luo","year":"2022","journal-title":"Mil. Med. Res."},{"key":"10.1016\/j.ygeno.2025.111082_bb0155","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1038\/cr.2013.74","article-title":"Restrictions to HIV-1 replication in resting CD4+ T lymphocytes","volume":"23","author":"Pan","year":"2013","journal-title":"Cell Res."},{"key":"10.1016\/j.ygeno.2025.111082_bb0160","doi-asserted-by":"crossref","first-page":"2042","DOI":"10.1038\/s41467-019-10023-4","article-title":"Akt and STAT5 mediate na\u00efve human CD4+ T-cell early metabolic response to TCR stimulation","volume":"10","author":"Jones","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ygeno.2025.111082_bb0165","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/s41577-019-0203-y","article-title":"Metabolic coordination of T cell quiescence and activation","volume":"20","author":"Chapman","year":"2020","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0170","first-page":"1","article-title":"The role of metabolic reprogramming in T cell fate and function","volume":"17","author":"Patsoukis","year":"2016","journal-title":"Current trends in immunology"},{"key":"10.1016\/j.ygeno.2025.111082_bb0175","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/j.cmet.2018.11.015","article-title":"Cellular metabolism is a major determinant of HIV-1 reservoir seeding in CD4(+) T cells and offers an opportunity to tackle infection","volume":"29","author":"Valle-Casuso","year":"2019","journal-title":"Cell Metab."},{"key":"10.1016\/j.ygeno.2025.111082_bb0180","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/nchembio.2384","article-title":"Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A","volume":"13","author":"Quinlan","year":"2017","journal-title":"Nat. Chem. Biol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0185","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1002\/hep.30671","article-title":"Circular RNA MAT2B promotes glycolysis and malignancy of hepatocellular carcinoma through the miR-338-3p\/PKM2 Axis under hypoxic stress","volume":"70","author":"Li","year":"2019","journal-title":"Hepatology (Baltimore, Md)"},{"key":"10.1016\/j.ygeno.2025.111082_bb0190","doi-asserted-by":"crossref","DOI":"10.1016\/j.redox.2020.101850","article-title":"The toxic side of one-carbon metabolism and epigenetics","volume":"40","author":"Morellato","year":"2021","journal-title":"Redox Biol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0195","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1016\/j.molcel.2017.02.026","article-title":"A metabolic function for phospholipid and histone methylation","volume":"66","author":"Ye","year":"2017","journal-title":"Mol. Cell"},{"key":"10.1016\/j.ygeno.2025.111082_bb0200","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/j.freeradbiomed.2025.04.004","article-title":"Oxidative stress and central metabolism pathways impact epigenetic modulation in inflammation and immune response","volume":"233","author":"Garc\u00eda-Gim\u00e9nez","year":"2025","journal-title":"Free Radic. Biol. Med."},{"key":"10.1016\/j.ygeno.2025.111082_bb0205","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.62644","article-title":"Glutamine deprivation triggers NAGK-dependent hexosamine salvage","volume":"10","author":"Campbell","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.ygeno.2025.111082_bb0210","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/s41586-022-05125-x","article-title":"Phosphorylation of muramyl peptides by NAGK is required for NOD2 activation","volume":"609","author":"Stafford","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2025.111082_bb0215","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1016\/j.cellsig.2016.04.012","article-title":"Reconstitution of TGFBR2 in HCT116 colorectal cancer cells causes increased LFNG expression and enhanced N-acetyl-d-glucosamine incorporation into Notch1","volume":"28","author":"Lee","year":"2016","journal-title":"Cell. Signal."},{"key":"10.1016\/j.ygeno.2025.111082_bb0220","doi-asserted-by":"crossref","DOI":"10.1016\/j.ebiom.2024.105338","article-title":"HIV-1-DNA\/RNA and immunometabolism in monocytes: contribution to the chronic immune activation and inflammation in people with HIV-1","volume":"108","author":"Mu\u00f1oz-Muela","year":"2024","journal-title":"EBioMedicine"},{"key":"10.1016\/j.ygeno.2025.111082_bb0225","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1093\/infdis\/jit581","article-title":"Evidence for innate immune system activation in HIV type 1-infected elite controllers","volume":"209","author":"Krishnan","year":"2014","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.ygeno.2025.111082_bb0230","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.883728","article-title":"NK cells, monocytes and macrophages in HIV-1 control: impact of innate immune responses","volume":"13","author":"Mensching","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0235","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/s41577-021-00649-1","article-title":"Engaging innate immunity in HIV-1 cure strategies","volume":"22","author":"Board","year":"2022","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0240","doi-asserted-by":"crossref","DOI":"10.1172\/JCI146136","article-title":"Long noncoding RNA MIR4435-2HG enhances metabolic function of myeloid dendritic cells from HIV-1 elite controllers","volume":"131","author":"Hartana","year":"2021","journal-title":"J. Clin. Invest."},{"key":"10.1016\/j.ygeno.2025.111082_bb0245","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1083\/jcb.201006121","article-title":"NADPH oxidase links endoplasmic reticulum stress, oxidative stress, and PKR activation to induce apoptosis","volume":"191","author":"Li","year":"2010","journal-title":"J. Cell Biol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0250","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/s41580-020-0230-3","article-title":"Reactive oxygen species (ROS) as pleiotropic physiological signalling agents","volume":"21","author":"Sies","year":"2020","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.ygeno.2025.111082_bb0255","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.ebiom.2019.03.004","article-title":"Immunometabolism is a key factor for the persistent spontaneous elite control of HIV-1 infection","volume":"42","author":"Tarancon-Diez","year":"2019","journal-title":"EBioMedicine"}],"container-title":["Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754325000989?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754325000989?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T15:23:04Z","timestamp":1765812184000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0888754325000989"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9]]},"references-count":51,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2025,9]]}},"alternative-id":["S0888754325000989"],"URL":"https:\/\/doi.org\/10.1016\/j.ygeno.2025.111082","relation":{},"ISSN":["0888-7543"],"issn-type":[{"value":"0888-7543","type":"print"}],"subject":[],"published":{"date-parts":[[2025,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Global transcriptome characterization of peripheral blood mononuclear cells in individuals with chronic HIV infection","name":"articletitle","label":"Article Title"},{"value":"Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ygeno.2025.111082","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"111082"}}