{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T18:06:10Z","timestamp":1784052370726,"version":"3.55.0"},"reference-count":82,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T00:00:00Z","timestamp":1783987200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010877","name":"ViiV Healthcare","doi-asserted-by":"publisher","award":["A18-1052"],"award-info":[{"award-number":["A18-1052"]}],"id":[{"id":"10.13039\/100010877","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    The spontaneous control of HIV infection in the absence of antiretroviral therapy, termed HIV control, is associated with genetic variation in the Major Histocompatibility Complex (MHC) locus. These variants are known to influence the immune response to HIV itself. However, people living with HIV are often co-infected with other pathogens that can also elicit immune responses, which might also be regulated by these variants. Here, we assessed whether genetic variants associated with HIV control influence cytokine responses to various co-pathogens. HIV-control-associated single nucleotide polymorphisms (SNPs) were enriched among variants regulating TNF-\u03b1 and IL-1\u03b2 production upon CMV pp65 peptide pool stimulation. The top enriched SNPs, rs1128175-A and rs2853971-A, were linked to lower odds of HIV control and increased cytokine responses to CMV. These SNPs were in linkage disequilibrium (LD) with classical HLA alleles HLA-B*07:02 and HLA-C*07:02. Intracellular cytokine staining showed CMV serostatus-dependent production of TNF-\u03b1 by monocytes and CD8 T cells. The rs1128175-A\/rs2853971-A\/HLA-B*07:02\/HLA-C*07:02 haplotype was associated with increased IFN-\u03b3 production by CD8 T cells upon CMV pp65 peptide pool stimulation, indicating an effect on memory responses. Quantitative trait locus (QTL) mapping showed that rs1128175 and rs2853971 influence\n                    <jats:italic>HLA-B<\/jats:italic>\n                    and\n                    <jats:italic>HLA-C<\/jats:italic>\n                    expression, DNA methylation levels and cell-type-specific cis-effects on chromatin accessibility, as well as CD8 T cell subset abundance. These QTL associations suggest that variants associated with poor HIV control are linked to heightened pro-inflammatory responses to CMV pp65 through effects on antigen presentation, epigenetic modifications, gene expression and immune cell repertoire, potentially negatively affecting HIV control status.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1014355","type":"journal-article","created":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T17:21:28Z","timestamp":1784049688000},"page":"e1014355","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Co-regulation of HIV control and cytomegalovirus pp65-specific IL-1\u03b2 and TNF-\u03b1 responses by genetic variants in the MHC region"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8846-957X","authenticated-orcid":true,"given":"Suzanne D. E.","family":"Ruijten","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9ssica C.","family":"dos Santos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Rios-Vazquez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriana","family":"Navas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanneke","family":"Maas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert L.","family":"Groenendijk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc J. T.","family":"Blaauw","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louise E.","family":"van Eekeren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wilhelm A. J. W.","family":"Vos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rainer","family":"Knoll","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manoj","family":"Kumar Gupta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rob","family":"ter Horst","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Javier","family":"Botey-Bataller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nienke","family":"van Unen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna C.","family":"Aschenbrenner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joachim L.","family":"Schultze","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng-Jian","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mihai G.","family":"Netea","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andre J. A. M.","family":"van der Ven","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5852-6801","authenticated-orcid":true,"given":"Vasiliki","family":"Matzaraki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,7,14]]},"reference":[{"issue":"9","key":"ppat.1014355.ref001","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1097\/QAD.0b013e32832b44c8","article-title":"Prevalence and comparative characteristics of long-term nonprogressors and HIV controller patients in the French Hospital Database on HIV","volume":"23","author":"S Grabar","year":"2009","journal-title":"AIDS"},{"issue":"11","key":"ppat.1014355.ref002","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.1086\/646609","article-title":"Clinical outcomes of elite controllers, viremic controllers, and long-term nonprogressors in the US Department of Defense HIV natural history study","volume":"200","author":"JF Okulicz","year":"2009","journal-title":"J Infect Dis"},{"key":"ppat.1014355.ref003","volume-title":"Global HIV & AIDS statistics - Fact Sheet","author":"UNAIDS","year":"2023"},{"issue":"13","key":"ppat.1014355.ref004","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1056\/NEJM200003303421303","article-title":"Viral load and heterosexual transmission of human immunodeficiency virus type 1","volume":"342","author":"TC Quinn","year":"2000","journal-title":"N Engl J Med"},{"issue":"2","key":"ppat.1014355.ref005","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1097\/QAD.0000000000000049","article-title":"A systematic review of definitions of extreme phenotypes of HIV control and progression","volume":"28","author":"D Gurdasani","year":"2014","journal-title":"AIDS"},{"issue":"6","key":"ppat.1014355.ref006","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1093\/infdis\/jiv148","article-title":"The sordid affair between human herpesvirus and HIV","volume":"212","author":"S Gianella","year":"2015","journal-title":"J Infect Dis"},{"issue":"2","key":"ppat.1014355.ref007","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/infdis\/jiu417","article-title":"Cytomegalovirus coinfection is associated with an increased risk of severe non-AIDS-defining events in a large cohort of HIV-infected patients","volume":"211","author":"M Lichtner","year":"2015","journal-title":"J Infect Dis"},{"key":"ppat.1014355.ref008","doi-asserted-by":"crossref","DOI":"10.1093\/infdis\/jiw217","article-title":"Cytomegalovirus and HIV: a dangerous Pas de Deux","volume":"214","author":"S Gianella","year":"2016","journal-title":"J Infect Dis"},{"issue":"5","key":"ppat.1014355.ref009","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1084\/jem.20050882","article-title":"Broadly targeted human cytomegalovirus-specific CD4+ and CD8+ T cells dominate the memory compartments of exposed subjects","volume":"202","author":"AW Sylwester","year":"2005","journal-title":"J Exp Med"},{"issue":"1","key":"ppat.1014355.ref010","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0008886","article-title":"Cytomegalovirus-specific T cells persist at very high levels during long-term antiretroviral treatment of HIV disease","volume":"5","author":"DM Naeger","year":"2010","journal-title":"PLoS One"},{"issue":"12","key":"ppat.1014355.ref011","doi-asserted-by":"crossref","first-page":"3664","DOI":"10.1182\/blood-2004-05-2058","article-title":"Imprint of human cytomegalovirus infection on the NK cell receptor repertoire","volume":"104","author":"M Gum\u00e1","year":"2004","journal-title":"Blood"},{"key":"ppat.1014355.ref012","doi-asserted-by":"crossref","DOI":"10.1089\/aid.2017.0145","article-title":"Cytomegalovirus and HIV persistence: pouring gas on the fire","volume":"33","author":"A Christensen-Quick","year":"2017","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"6010","key":"ppat.1014355.ref013","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1126\/science.1195271","article-title":"The international HIV controllers study. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation","volume":"330","author":"International HIV Controllers Study","year":"2010","journal-title":"Science"},{"issue":"47","key":"ppat.1014355.ref014","doi-asserted-by":"crossref","first-page":"14658","DOI":"10.1073\/pnas.1514867112","article-title":"Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load","volume":"112","author":"PJ McLaren","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7","key":"ppat.1014355.ref015","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003515","article-title":"Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls","volume":"9","author":"PJ McLaren","year":"2013","journal-title":"PLOS 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Santos","year":"2026","journal-title":"iScience"},{"issue":"5","key":"ppat.1014355.ref032","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1111\/tan.15089","article-title":"The influence of HLA A, B, C, DR alleles and HLA haplotypes on cytomegalovirus-specific cell mediated immunity in seropositive Korean kidney transplant candidates","volume":"102","author":"H Lee","year":"2023","journal-title":"HLA"},{"issue":"6","key":"ppat.1014355.ref033","doi-asserted-by":"crossref","first-page":"1676","DOI":"10.1002\/1521-4141(200006)30:6<1676::AID-IMMU1676>3.0.CO;2-V","article-title":"Analysis of CD8 T cell reactivity to cytomegalovirus using protein-spanning pools of overlapping pentadecapeptides","volume":"30","author":"F Kern","year":"2000","journal-title":"Eur J Immunol"},{"issue":"5","key":"ppat.1014355.ref034","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003383","article-title":"Presentation of an immunodominant immediate-early CD8+ T cell epitope resists human 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treatment","volume":"88","author":"S Gianella","year":"2014","journal-title":"J Virol"},{"issue":"8","key":"ppat.1014355.ref041","doi-asserted-by":"crossref","DOI":"10.1093\/ofid\/ofaa289","article-title":"Sex differences in CMV replication and HIV persistence during suppressive ART","volume":"7","author":"S Gianella","year":"2020","journal-title":"Open Forum Infect Dis"},{"key":"ppat.1014355.ref042","doi-asserted-by":"crossref","first-page":"130","DOI":"10.3389\/fcimb.2020.00130","article-title":"Cytomegalovirus latency and reactivation: an intricate interplay with the host immune response","volume":"10","author":"E Forte","year":"2020","journal-title":"Front Cell Infect Microbiol"},{"key":"ppat.1014355.ref043","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1146\/annurev.immunol.021908.132612","article-title":"Immunological and inflammatory functions of the interleukin-1 family","volume":"27","author":"CA Dinarello","year":"2009","journal-title":"Annu Rev Immunol"},{"key":"ppat.1014355.ref044","doi-asserted-by":"crossref","first-page":"15402","DOI":"10.1038\/ncomms15402","article-title":"Antigen-specific CD8+ T cell feedback activates NLRP3 inflammasome in antigen-presenting cells through perforin","volume":"8","author":"Y Yao","year":"2017","journal-title":"Nat Commun"},{"issue":"9","key":"ppat.1014355.ref045","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/s41577-018-0029-z","article-title":"IFN\u03b3: signalling, epigenetics and roles in immunity, metabolism, disease and cancer immunotherapy","volume":"18","author":"LB Ivashkiv","year":"2018","journal-title":"Nat Rev Immunol"},{"issue":"1","key":"ppat.1014355.ref046","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1080\/00015550410023527","article-title":"HLA-Cw*0602 associates more strongly to psoriasis in the Swedish population than variants of the novel 6p21.3 gene PSORS1C3","volume":"85","author":"SJ Holm","year":"2005","journal-title":"Acta Derm 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Hansen","year":"2011","journal-title":"Nature"},{"key":"ppat.1014355.ref059","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.imlet.2016.05.001","article-title":"IL-17+ CD8+ T cells: differentiation, phenotype and role in inflammatory disease","volume":"178","author":"U Srenathan","year":"2016","journal-title":"Immunol Lett"},{"issue":"8","key":"ppat.1014355.ref060","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nm.4140","article-title":"Understanding human immune function using the resources from the Human Functional Genomics Project","volume":"22","author":"MG Netea","year":"2016","journal-title":"Nat Med"},{"key":"ppat.1014355.ref061","doi-asserted-by":"crossref","first-page":"982746","DOI":"10.3389\/fimmu.2022.982746","article-title":"The 2000HIV study: Design, multi-omics methods and participant characteristics","volume":"13","author":"WAJW Vos","year":"2022","journal-title":"Front 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