{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T06:45:06Z","timestamp":1792737906316,"version":"4.5.0"},"reference-count":73,"publisher":"National Academy of Sciences","issue":"50","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2012,12,11]]},"abstract":"<jats:p>\n                    To better understand how innate immune responses to vaccination can lead to lasting protective immunity, we used a systems approach to define immune signatures in humans over 1 wk following MRKAd5\/HIV vaccination that predicted subsequent HIV-specific T-cell responses. Within 24 h, striking increases in peripheral blood mononuclear cell gene expression associated with inflammation, IFN response, and myeloid cell trafficking occurred, and lymphocyte-specific transcripts decreased. These alterations were corroborated by marked serum inflammatory cytokine elevations and egress of circulating lymphocytes. Responses of vaccinees with preexisting adenovirus serotype 5 (Ad5) neutralizing antibodies were strongly attenuated, suggesting that enhanced HIV acquisition in Ad5-seropositive subgroups in the Step Study may relate to the lack of appropriate innate activation rather than to increased systemic immune activation. Importantly, patterns of chemoattractant cytokine responses at 24 h and alterations in 209 peripheral blood mononuclear cell transcripts at 72 h were predictive of subsequent induction and magnitude of HIV-specific CD8\n                    <jats:sup>+<\/jats:sup>\n                    T-cell responses. This systems approach provides a framework to compare innate responses induced by vectors, as shown here by contrasting the more rapid, robust response to MRKAd5\/HIV with that to yellow fever vaccine. When applied iteratively, the findings may permit selection of HIV vaccine candidates eliciting innate immune response profiles more likely to drive HIV protective immunity.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1208972109","type":"journal-article","created":{"date-parts":[[2012,11,14]],"date-time":"2012-11-14T23:45:26Z","timestamp":1352936726000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":156,"title":["Merck Ad5\/HIV induces broad innate immune activation that predicts CD8\n                    <sup>+<\/sup>\n                    T-cell responses but is attenuated by preexisting Ad5 immunity"],"prefix":"10.1073","volume":"109","author":[{"given":"Daniel E.","family":"Zak","sequence":"first","affiliation":[{"name":"Seattle Biomedical Research Institute, Seattle, WA 98109;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erica","family":"Andersen-Nissen","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric R.","family":"Peterson","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alicia","family":"Sato","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Kristina","family":"Hamilton","sequence":"additional","affiliation":[{"name":"Seattle Biomedical Research Institute, Seattle, WA 98109;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joleen","family":"Borgerding","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akshay T.","family":"Krishnamurty","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne T.","family":"Chang","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devin J.","family":"Adams","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiffany R.","family":"Hensley","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander I.","family":"Salter","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cecilia A.","family":"Morgan","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"},{"name":"HIV Vaccine Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ann C.","family":"Duerr","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"},{"name":"HIV Vaccine Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen C.","family":"De Rosa","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"},{"name":"HIV Vaccine Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and"},{"name":"Department of Laboratory Medicine,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan","family":"Aderem","sequence":"additional","affiliation":[{"name":"Seattle Biomedical Research Institute, Seattle, WA 98109;"},{"name":"Department of Immunology, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Juliana","family":"McElrath","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division and"},{"name":"HIV Vaccine Trials Network, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and"},{"name":"Department of Medicine, University of Washington, Seattle, WA 98195"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2012,11,14]]},"reference":[{"key":"e_1_1_2_17_11_1_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa0908492"},{"key":"e_1_1_2_17_11_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(08)61592-5"},{"key":"e_1_1_2_17_11_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/nm.2316"},{"key":"e_1_1_2_17_11_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature10124"},{"key":"e_1_1_2_17_11_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/ni.1688"},{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"2209","DOI":"10.1056\/NEJMoa0908492","article-title":"Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand","volume":"361","author":"Rerks-Ngarm S","year":"2009","unstructured":"S Rerks-Ngarm, et al., Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N Engl J Med; MOPH-TAVEG Investigators 361, 2209\u20132220 (2009).","journal-title":"N Engl J Med"},{"key":"e_1_3_4_2_2","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/ni.2039","article-title":"Immunological mechanisms of vaccination","volume":"12","author":"Pulendran B","year":"2011","unstructured":"B Pulendran, R Ahmed, Immunological mechanisms of vaccination. Nat Immunol 12, 509\u2013517 (2011).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_3_2","doi-asserted-by":"crossref","first-page":"1894","DOI":"10.1016\/S0140-6736(08)61592-5","article-title":"HIV-1 vaccine-induced immunity in the test-of-concept Step Study: A case-cohort analysis","volume":"372","author":"McElrath MJ","year":"2008","unstructured":"MJ McElrath, et al., HIV-1 vaccine-induced immunity in the test-of-concept Step Study: A case-cohort analysis. Lancet; Step Study Protocol Team 372, 1894\u20131905 (2008).","journal-title":"Lancet"},{"key":"e_1_3_4_4_2","doi-asserted-by":"crossref","first-page":"1881","DOI":"10.1016\/S0140-6736(08)61591-3","article-title":"Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): A double-blind, randomised, placebo-controlled, test-of-concept trial","volume":"372","author":"Buchbinder SP","year":"2008","unstructured":"SP Buchbinder, et al., Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): A double-blind, randomised, placebo-controlled, test-of-concept trial. Lancet; Step Study Protocol Team 372, 1881\u20131893 (2008).","journal-title":"Lancet"},{"key":"e_1_3_4_5_2","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/S1473-3099(11)70098-6","article-title":"Safety and efficacy of the HVTN 503\/Phambili study of a clade-B-based HIV-1 vaccine in South Africa: A double-blind, randomised, placebo-controlled test-of-concept phase 2b study","volume":"11","author":"Gray GE","year":"2011","unstructured":"GE Gray, et al., Safety and efficacy of the HVTN 503\/Phambili study of a clade-B-based HIV-1 vaccine in South Africa: A double-blind, randomised, placebo-controlled test-of-concept phase 2b study. Lancet Infect Dis; HVTN 503\/Phambili study team 11, 507\u2013515 (2011).","journal-title":"Lancet Infect Dis"},{"key":"e_1_3_4_6_2","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/nm.2316","article-title":"Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial","volume":"17","author":"Rolland M","year":"2011","unstructured":"M Rolland, et al., Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial. Nat Med 17, 366\u2013371 (2011).","journal-title":"Nat Med"},{"key":"e_1_3_4_7_2","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1038\/nm.1989","article-title":"Baseline Ad5 serostatus does not predict Ad5 HIV vaccine-induced expansion of adenovirus-specific CD4+ T cells","volume":"15","author":"Hutnick NA","year":"2009","unstructured":"NA Hutnick, et al., Baseline Ad5 serostatus does not predict Ad5 HIV vaccine-induced expansion of adenovirus-specific CD4+ T cells. Nat Med 15, 876\u2013878 (2009).","journal-title":"Nat Med"},{"key":"e_1_3_4_8_2","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1038\/nm.1991","article-title":"Adenovirus-specific immunity after immunization with an Ad5 HIV-1 vaccine candidate in humans","volume":"15","author":"O\u2019Brien KL","year":"2009","unstructured":"KL O\u2019Brien, et al., Adenovirus-specific immunity after immunization with an Ad5 HIV-1 vaccine candidate in humans. Nat Med 15, 873\u2013875 (2009).","journal-title":"Nat Med"},{"key":"e_1_3_4_9_2","doi-asserted-by":"crossref","first-page":"2239","DOI":"10.1128\/JVI.06175-11","article-title":"Low-dose penile SIVmac251 exposure of rhesus macaques infected with adenovirus type 5 (Ad5) and then immunized with a replication-defective Ad5-based SIV gag\/pol\/nef vaccine recapitulates the results of the phase IIb step trial of a similar HIV-1 vaccine","volume":"86","author":"Qureshi H","year":"2012","unstructured":"H Qureshi, et al., Low-dose penile SIVmac251 exposure of rhesus macaques infected with adenovirus type 5 (Ad5) and then immunized with a replication-defective Ad5-based SIV gag\/pol\/nef vaccine recapitulates the results of the phase IIb step trial of a similar HIV-1 vaccine. J Virol 86, 2239\u20132250 (2012).","journal-title":"J Virol"},{"key":"e_1_3_4_10_2","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1038\/nm.2447","article-title":"CD8+ cellular immunity mediates rAd5 vaccine protection against Ebola virus infection of nonhuman primates","volume":"17","author":"Sullivan NJ","year":"2011","unstructured":"NJ Sullivan, et al., CD8+ cellular immunity mediates rAd5 vaccine protection against Ebola virus infection of nonhuman primates. Nat Med 17, 1128\u20131131 (2011).","journal-title":"Nat Med"},{"key":"e_1_3_4_11_2","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1038\/mt.2009.60","article-title":"Immunization with a bivalent adenovirus-vectored tuberculosis vaccine provides markedly improved protection over its monovalent counterpart against pulmonary tuberculosis","volume":"17","author":"Mu J","year":"2009","unstructured":"J Mu, et al., Immunization with a bivalent adenovirus-vectored tuberculosis vaccine provides markedly improved protection over its monovalent counterpart against pulmonary tuberculosis. Mol Ther 17, 1093\u20131100 (2009).","journal-title":"Mol Ther"},{"key":"e_1_3_4_12_2","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1097\/COH.0b013e32834ddcd9","article-title":"Profiling immunity to HIV vaccines with systems biology","volume":"7","author":"Andersen-Nissen E","year":"2012","unstructured":"E Andersen-Nissen, A Heit, MJ McElrath, Profiling immunity to HIV vaccines with systems biology. Curr Opin HIV AIDS 7, 32\u201337 (2012).","journal-title":"Curr Opin HIV AIDS"},{"key":"e_1_3_4_13_2","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1097\/COH.0b013e32834ddd31","article-title":"Overcoming limitations in the systems vaccinology approach: A pathway for accelerated HIV vaccine development","volume":"7","author":"Zak DE","year":"2012","unstructured":"DE Zak, A Aderem, Overcoming limitations in the systems vaccinology approach: A pathway for accelerated HIV vaccine development. Curr Opin HIV AIDS 7, 58\u201363 (2012).","journal-title":"Curr Opin HIV AIDS"},{"key":"e_1_3_4_14_2","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nature04768","article-title":"Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4","volume":"441","author":"Gilchrist M","year":"2006","unstructured":"M Gilchrist, et al., Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441, 173\u2013178 (2006).","journal-title":"Nature"},{"key":"e_1_3_4_15_2","doi-asserted-by":"crossref","first-page":"e1000021","DOI":"10.1371\/journal.pcbi.1000021","article-title":"Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics","volume":"4","author":"Ramsey SA","year":"2008","unstructured":"SA Ramsey, et al., Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLOS Comput Biol 4, e1000021 (2008).","journal-title":"PLOS Comput Biol"},{"key":"e_1_3_4_16_2","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/ni.1721","article-title":"Function of C\/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals","volume":"10","author":"Litvak V","year":"2009","unstructured":"V Litvak, et al., Function of C\/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol 10, 437\u2013443 (2009).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_17_2","doi-asserted-by":"crossref","first-page":"11536","DOI":"10.1073\/pnas.1107577108","article-title":"Systems analysis identifies an essential role for SHANK-associated RH domain-interacting protein (SHARPIN) in macrophage Toll-like receptor 2 (TLR2) responses","volume":"108","author":"Zak DE","year":"2011","unstructured":"DE Zak, et al., Systems analysis identifies an essential role for SHANK-associated RH domain-interacting protein (SHARPIN) in macrophage Toll-like receptor 2 (TLR2) responses. Proc Natl Acad Sci USA 108, 11536\u201311541 (2011).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_18_2","doi-asserted-by":"crossref","first-page":"3119","DOI":"10.1084\/jem.20082292","article-title":"Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses","volume":"205","author":"Gaucher D","year":"2008","unstructured":"D Gaucher, et al., Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med 205, 3119\u20133131 (2008).","journal-title":"J Exp Med"},{"key":"e_1_3_4_19_2","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/ni.1688","article-title":"Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans","volume":"10","author":"Querec TD","year":"2009","unstructured":"TD Querec, et al., Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol 10, 116\u2013125 (2009).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_20_2","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1038\/ni.2067","article-title":"Systems biology of vaccination for seasonal influenza in humans","volume":"12","author":"Nakaya HI","year":"2011","unstructured":"HI Nakaya, et al., Systems biology of vaccination for seasonal influenza in humans. Nat Immunol 12, 786\u2013795 (2011).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_21_2","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.immuni.2008.05.012","article-title":"A modular analysis framework for blood genomics studies: Application to systemic lupus erythematosus","volume":"29","author":"Chaussabel D","year":"2008","unstructured":"D Chaussabel, et al., A modular analysis framework for blood genomics studies: Application to systemic lupus erythematosus. Immunity 29, 150\u2013164 (2008).","journal-title":"Immunity"},{"key":"e_1_3_4_22_2","doi-asserted-by":"crossref","first-page":"e34390","DOI":"10.1371\/journal.pone.0034390","article-title":"Host immune transcriptional profiles reflect the variability in clinical disease manifestations in patients with Staphylococcus aureus infections","volume":"7","author":"Banchereau R","year":"2012","unstructured":"R Banchereau, et al., Host immune transcriptional profiles reflect the variability in clinical disease manifestations in patients with Staphylococcus aureus infections. PLoS ONE 7, e34390 (2012).","journal-title":"PLoS ONE"},{"key":"e_1_3_4_23_2","first-page":"A1","article-title":"P01.06: Whole blood transcriptional monitoring of acute HIV-1 infection reveals differential signatures of host immune activation","volume":"27","author":"Skinner JA","year":"2011","unstructured":"JA Skinner, et al., P01.06: Whole blood transcriptional monitoring of acute HIV-1 infection reveals differential signatures of host immune activation. AIDS Res Hum Retroviruses 27, A1\u2013A148 (2011).","journal-title":"AIDS Res Hum Retroviruses"},{"key":"e_1_3_4_24_2","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.1200\/JCO.2004.04.059","article-title":"Phase I trial of intratumoral injection of an adenovirus encoding interleukin-12 for advanced digestive tumors","volume":"22","author":"Sangro B","year":"2004","unstructured":"B Sangro, et al., Phase I trial of intratumoral injection of an adenovirus encoding interleukin-12 for advanced digestive tumors. J Clin Oncol 22, 1389\u20131397 (2004).","journal-title":"J Clin Oncol"},{"key":"e_1_3_4_25_2","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1038\/nri3070","article-title":"Monocyte recruitment during infection and inflammation","volume":"11","author":"Shi C","year":"2011","unstructured":"C Shi, EG Pamer, Monocyte recruitment during infection and inflammation. Nat Rev Immunol 11, 762\u2013774 (2011).","journal-title":"Nat Rev Immunol"},{"key":"e_1_3_4_26_2","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1016\/j.immuni.2008.11.004","article-title":"Memory T cell RNA rearrangement programmed by heterogeneous nuclear ribonucleoprotein hnRNPLL","volume":"29","author":"Wu Z","year":"2008","unstructured":"Z Wu, et al., Memory T cell RNA rearrangement programmed by heterogeneous nuclear ribonucleoprotein hnRNPLL. Immunity 29, 863\u2013875 (2008).","journal-title":"Immunity"},{"key":"e_1_3_4_27_2","doi-asserted-by":"crossref","first-page":"2366","DOI":"10.1038\/nprot.2007.324","article-title":"Integration of biological networks and gene expression data using Cytoscape","volume":"2","author":"Cline MS","year":"2007","unstructured":"MS Cline, et al., Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2, 2366\u20132382 (2007).","journal-title":"Nat Protoc"},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1016\/j.molimm.2003.11.024","article-title":"The LLT1 receptor induces IFN-gamma production by human natural killer cells","volume":"40","author":"Mathew PA","year":"2004","unstructured":"PA Mathew, et al., The LLT1 receptor induces IFN-gamma production by human natural killer cells. Mol Immunol 40, 1157\u20131163 (2004).","journal-title":"Mol Immunol"},{"key":"e_1_3_4_29_2","doi-asserted-by":"crossref","first-page":"5683","DOI":"10.4049\/jimmunol.1001974","article-title":"Cutting edge: The adapters EAT-2A and -2B are positive regulators of CD244- and CD84-dependent NK cell functions in the C57BL\/6 mouse","volume":"185","author":"Wang N","year":"2010","unstructured":"N Wang, et al., Cutting edge: The adapters EAT-2A and -2B are positive regulators of CD244- and CD84-dependent NK cell functions in the C57BL\/6 mouse. J Immunol 185, 5683\u20135687 (2010).","journal-title":"J Immunol"},{"key":"e_1_3_4_30_2","doi-asserted-by":"crossref","first-page":"722","DOI":"10.4049\/jimmunol.1002105","article-title":"Expression of the SLAM family of receptors adapter EAT-2 as a novel strategy for enhancing beneficial immune responses to vaccine antigens","volume":"186","author":"Aldhamen YA","year":"2011","unstructured":"YA Aldhamen, et al., Expression of the SLAM family of receptors adapter EAT-2 as a novel strategy for enhancing beneficial immune responses to vaccine antigens. J Immunol 186, 722\u2013732 (2011).","journal-title":"J Immunol"},{"key":"e_1_3_4_31_2","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1038\/nri2629","article-title":"Learning immunology from the yellow fever vaccine: Innate immunity to systems vaccinology","volume":"9","author":"Pulendran B","year":"2009","unstructured":"B Pulendran, Learning immunology from the yellow fever vaccine: Innate immunity to systems vaccinology. Nat Rev Immunol 9, 741\u2013747 (2009).","journal-title":"Nat Rev Immunol"},{"key":"e_1_3_4_32_2","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1084\/jem.20051720","article-title":"Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity","volume":"203","author":"Querec T","year":"2006","unstructured":"T Querec, et al., Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity. J Exp Med 203, 413\u2013424 (2006).","journal-title":"J Exp Med"},{"key":"e_1_3_4_33_2","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/ni.1693","article-title":"Influence of CRACC, a SLAM family receptor coupled to the adaptor EAT-2, on natural killer cell function","volume":"10","author":"Cruz-Munoz ME","year":"2009","unstructured":"ME Cruz-Munoz, Z Dong, X Shi, S Zhang, A Veillette, Influence of CRACC, a SLAM family receptor coupled to the adaptor EAT-2, on natural killer cell function. Nat Immunol 10, 297\u2013305 (2009).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_34_2","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.bbrc.2005.08.232","article-title":"Indoleamine 2,3 dioxygenase and regulation of T cell immunity","volume":"338","author":"Mellor A","year":"2005","unstructured":"A Mellor, Indoleamine 2,3 dioxygenase and regulation of T cell immunity. Biochem Biophys Res Commun 338, 20\u201324 (2005).","journal-title":"Biochem Biophys Res Commun"},{"key":"e_1_3_4_35_2","doi-asserted-by":"crossref","first-page":"2736","DOI":"10.1172\/JCI45444","article-title":"Kr\u00fcppel-like factor 4 regulates macrophage polarization","volume":"121","author":"Liao X","year":"2011","unstructured":"X Liao, et al., Kr\u00fcppel-like factor 4 regulates macrophage polarization. J Clin Invest 121, 2736\u20132749 (2011).","journal-title":"J Clin Invest"},{"key":"e_1_3_4_36_2","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1182\/blood-2005-09-3556","article-title":"Mutation of mouse Mayp\/Pstpip2 causes a macrophage autoinflammatory disease","volume":"107","author":"Grosse J","year":"2006","unstructured":"J Grosse, et al., Mutation of mouse Mayp\/Pstpip2 causes a macrophage autoinflammatory disease. Blood 107, 3350\u20133358 (2006).","journal-title":"Blood"},{"key":"e_1_3_4_37_2","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.gene.2011.07.004","article-title":"Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes","volume":"487","author":"Shi L","year":"2011","unstructured":"L Shi, JC Perin, J Leipzig, Z Zhang, KE Sullivan, Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes. Gene 487, 21\u201328 (2011).","journal-title":"Gene"},{"key":"e_1_3_4_38_2","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2008.04.043","article-title":"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells","volume":"133","author":"Chen X","year":"2008","unstructured":"X Chen, et al., Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106\u20131117 (2008).","journal-title":"Cell"},{"key":"e_1_3_4_39_2","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1038\/ni.1656","article-title":"Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression","volume":"9","author":"Liao W","year":"2008","unstructured":"W Liao, et al., Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression. Nat Immunol 9, 1288\u20131296 (2008).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_40_2","doi-asserted-by":"crossref","first-page":"2717","DOI":"10.1084\/jem.20081786","article-title":"Activation of a dendritic cell-T cell axis by Ad5 immune complexes creates an improved environment for replication of HIV in T cells","volume":"205","author":"Perreau M","year":"2008","unstructured":"M Perreau, G Pantaleo, EJ Kremer, Activation of a dendritic cell-T cell axis by Ad5 immune complexes creates an improved environment for replication of HIV in T cells. J Exp Med 205, 2717\u20132725 (2008).","journal-title":"J Exp Med"},{"key":"e_1_3_4_41_2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1097\/QAD.0b013e32830e6d6d","article-title":"Post-step modifications for research on HIV vaccines","volume":"23","author":"Corey L","year":"2009","unstructured":"L Corey, MJ McElrath, JG Kublin, Post-step modifications for research on HIV vaccines. AIDS 23, 3\u20138 (2009).","journal-title":"AIDS"},{"key":"e_1_3_4_42_2","doi-asserted-by":"crossref","first-page":"19940","DOI":"10.1073\/pnas.0907898106","article-title":"Adenovirus vector vaccination induces expansion of memory CD4 T cells with a mucosal homing phenotype that are readily susceptible to HIV-1","volume":"106","author":"Benlahrech A","year":"2009","unstructured":"A Benlahrech, et al., Adenovirus vector vaccination induces expansion of memory CD4 T cells with a mucosal homing phenotype that are readily susceptible to HIV-1. Proc Natl Acad Sci USA 106, 19940\u201319945 (2009).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_43_2","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1097\/QAI.0b013e31821acb5","article-title":"Impact of herpes simplex virus type 2 on HIV-1 acquisition and progression in an HIV vaccine trial (the Step study)","volume":"57","author":"Barnabas RV","year":"2011","unstructured":"RV Barnabas, et al., Impact of herpes simplex virus type 2 on HIV-1 acquisition and progression in an HIV vaccine trial (the Step study). J Acquir Immune Defic Syndr; NIAID HIV Vaccine Trials Network 57, 238\u2013244 (2011).","journal-title":"J Acquir Immune Defic Syndr"},{"key":"e_1_3_4_44_2","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1097\/QAD.0b013e328342115c","article-title":"Serological immunity to adenovirus serotype 5 is not associated with risk of HIV infection: A case-control study","volume":"25","author":"Curlin ME","year":"2011","unstructured":"ME Curlin, et al., Serological immunity to adenovirus serotype 5 is not associated with risk of HIV infection: A case-control study. AIDS 25, 153\u2013158 (2011).","journal-title":"AIDS"},{"key":"e_1_3_4_45_2","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1172\/JCI60202","article-title":"Human adenovirus-specific T cells modulate HIV-specific T cell responses to an Ad5-vectored HIV-1 vaccine","volume":"122","author":"Frahm N","year":"2012","unstructured":"N Frahm, et al., Human adenovirus-specific T cells modulate HIV-specific T cell responses to an Ad5-vectored HIV-1 vaccine. J Clin Invest 122, 359\u2013367 (2012).","journal-title":"J Clin Invest"},{"key":"e_1_3_4_46_2","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/sj.gt.3302152","article-title":"Inhibition of costimulation allows for repeated systemic administration of adenoviral vector in rhesus monkeys","volume":"11","author":"Haegel-Kronenberger H","year":"2004","unstructured":"H Haegel-Kronenberger, et al., Inhibition of costimulation allows for repeated systemic administration of adenoviral vector in rhesus monkeys. Gene Ther 11, 241\u2013252 (2004).","journal-title":"Gene Ther"},{"key":"e_1_3_4_47_2","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1096\/fasebj.8.13.7926371","article-title":"Monocyte chemotactic proteins MCP-1, MCP-2, and MCP-3 are major attractants for human CD4+ and CD8+ T lymphocytes","volume":"8","author":"Loetscher P","year":"1994","unstructured":"P Loetscher, M Seitz, I Clark-Lewis, M Baggiolini, B Moser, Monocyte chemotactic proteins MCP-1, MCP-2, and MCP-3 are major attractants for human CD4+ and CD8+ T lymphocytes. FASEB J 8, 1055\u20131060 (1994).","journal-title":"FASEB J"},{"key":"e_1_3_4_48_2","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1172\/JCI3986","article-title":"CD8 positive T cells influence antigen-specific immune responses through the expression of chemokines","volume":"102","author":"Kim JJ","year":"1998","unstructured":"JJ Kim, et al., CD8 positive T cells influence antigen-specific immune responses through the expression of chemokines. J Clin Invest 102, 1112\u20131124 (1998).","journal-title":"J Clin Invest"},{"key":"e_1_3_4_49_2","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1146\/annurev-immunol-031210-101312","article-title":"Regulation and functions of the IL-10 family of cytokines in inflammation and disease","volume":"29","author":"Ouyang W","year":"2011","unstructured":"W Ouyang, S Rutz, NK Crellin, PA Valdez, SG Hymowitz, Regulation and functions of the IL-10 family of cytokines in inflammation and disease. Annu Rev Immunol 29, 71\u2013109 (2011).","journal-title":"Annu Rev Immunol"},{"key":"e_1_3_4_50_2","doi-asserted-by":"crossref","first-page":"11515","DOI":"10.1128\/JVI.01703-09","article-title":"Lambda interferon is the predominant interferon induced by influenza A virus infection in vivo","volume":"84","author":"Jewell NA","year":"2010","unstructured":"NA Jewell, et al., Lambda interferon is the predominant interferon induced by influenza A virus infection in vivo. J Virol 84, 11515\u201311522 (2010).","journal-title":"J Virol"},{"key":"e_1_3_4_51_2","doi-asserted-by":"crossref","first-page":"8592","DOI":"10.1128\/MCB.21.24.8592-8604.2001","article-title":"Identification and characterization of thymus LIM protein: Targeted disruption reduces thymus cellularity","volume":"21","author":"Kirchner J","year":"2001","unstructured":"J Kirchner, KA Forbush, MJ Bevan, Identification and characterization of thymus LIM protein: Targeted disruption reduces thymus cellularity. Mol Cell Biol 21, 8592\u20138604 (2001).","journal-title":"Mol Cell Biol"},{"key":"e_1_3_4_52_2","doi-asserted-by":"crossref","first-page":"34010","DOI":"10.1074\/jbc.M205883200","article-title":"Identification of a neuropeptide modified with bromine as an endogenous ligand for GPR7","volume":"277","author":"Fujii R","year":"2002","unstructured":"R Fujii, et al., Identification of a neuropeptide modified with bromine as an endogenous ligand for GPR7. J Biol Chem 277, 34010\u201334016 (2002).","journal-title":"J Biol Chem"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1080\/15376510802312464","article-title":"Biodistribution and toxicological safety of adenovirus type 5 and type 35 vectored vaccines against human immunodeficiency virus-1 (HIV-1), Ebola, or Marburg are similar despite differing adenovirus serotype vector, manufacturer\u2019s construct, or gene inserts","volume":"5","author":"Sheets RL","year":"2008","unstructured":"RL Sheets, et al., Biodistribution and toxicological safety of adenovirus type 5 and type 35 vectored vaccines against human immunodeficiency virus-1 (HIV-1), Ebola, or Marburg are similar despite differing adenovirus serotype vector, manufacturer\u2019s construct, or gene inserts. J Immunotoxicol 5, 315\u2013335 (2008).","journal-title":"J Immunotoxicol"},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/S1074-7613(00)80262-9","article-title":"Regulation of LMP2 and TAP1 genes by IRF-1 explains the paucity of CD8+ T cells in IRF-1-\/- mice","volume":"5","author":"White LC","year":"1996","unstructured":"LC White, et al., Regulation of LMP2 and TAP1 genes by IRF-1 explains the paucity of CD8+ T cells in IRF-1-\/- mice. Immunity 5, 365\u2013376 (1996).","journal-title":"Immunity"},{"key":"e_1_3_4_55_2","first-page":"17","article-title":"Role of PD-1 in regulating T-cell immunity","volume":"350","author":"Jin HT","year":"2011","unstructured":"HT Jin, R Ahmed, T Okazaki, Role of PD-1 in regulating T-cell immunity. Curr Top Microbiol Immunol 350, 17\u201337 (2011).","journal-title":"Curr Top Microbiol Immunol"},{"key":"e_1_3_4_56_2","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1038\/nri1457","article-title":"IDO expression by dendritic cells: Tolerance and tryptophan catabolism","volume":"4","author":"Mellor AL","year":"2004","unstructured":"AL Mellor, DH Munn, IDO expression by dendritic cells: Tolerance and tryptophan catabolism. Nat Rev Immunol 4, 762\u2013774 (2004).","journal-title":"Nat Rev Immunol"},{"key":"e_1_3_4_57_2","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.jim.2007.02.003","article-title":"Defining blood processing parameters for optimal detection of cryopreserved antigen-specific responses for HIV vaccine trials","volume":"322","author":"Bull M","year":"2007","unstructured":"M Bull, et al., Defining blood processing parameters for optimal detection of cryopreserved antigen-specific responses for HIV vaccine trials. J Immunol Methods 322, 57\u201369 (2007).","journal-title":"J Immunol Methods"},{"key":"e_1_3_4_58_2","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.jim.2012.05.011","article-title":"Optimization and qualification of a multiplex bead array to assess cytokine and chemokine production by vaccine-specific cells","volume":"382","author":"Defawe OD","year":"2012","unstructured":"OD Defawe, et al., Optimization and qualification of a multiplex bead array to assess cytokine and chemokine production by vaccine-specific cells. J Immunol Methods 382, 117\u2013128 (2012).","journal-title":"J Immunol Methods"},{"key":"e_1_3_4_59_2","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1093\/biomet\/75.4.800","article-title":"A sharper Bonferroni procedure for multiple tests of significance","volume":"75","author":"Hochberg Y","year":"1988","unstructured":"Y Hochberg, A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75, 800\u2013802 (1988).","journal-title":"Biometrika"},{"key":"e_1_3_4_60_2","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/415331a","article-title":"Replication-incompetent adenoviral vaccine vector elicits effective anti-immunodeficiency-virus immunity","volume":"415","author":"Shiver JW","year":"2002","unstructured":"JW Shiver, et al., Replication-incompetent adenoviral vaccine vector elicits effective anti-immunodeficiency-virus immunity. Nature 415, 331\u2013335 (2002).","journal-title":"Nature"},{"key":"e_1_3_4_61_2","first-page":"285","article-title":"Transcription of infectious yellow fever RNA from full-length cDNA templates produced by in vitro ligation","volume":"1","author":"Rice CM","year":"1989","unstructured":"CM Rice, A Grakoui, R Galler, TJ Chambers, Transcription of infectious yellow fever RNA from full-length cDNA templates produced by in vitro ligation. New Biol 1, 285\u2013296 (1989).","journal-title":"New Biol"},{"key":"e_1_3_4_62_2","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1099\/vir.0.18860-0","article-title":"A stable full-length yellow fever virus cDNA clone and the role of conserved RNA elements in flavivirus replication","volume":"84","author":"Bredenbeek PJ","year":"2003","unstructured":"PJ Bredenbeek, et al., A stable full-length yellow fever virus cDNA clone and the role of conserved RNA elements in flavivirus replication. J Gen Virol 84, 1261\u20131268 (2003).","journal-title":"J Gen Virol"},{"key":"e_1_3_4_63_2","doi-asserted-by":"crossref","first-page":"5676","DOI":"10.1016\/j.vaccine.2010.06.052","article-title":"Evaluation of yellow fever virus 17D strain as a new vector for HIV-1 vaccine development","volume":"28","author":"Franco D","year":"2010","unstructured":"D Franco, et al., Evaluation of yellow fever virus 17D strain as a new vector for HIV-1 vaccine development. Vaccine 28, 5676\u20135685 (2010).","journal-title":"Vaccine"},{"key":"e_1_3_4_64_2","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1038\/nature09247","article-title":"An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis","volume":"466","author":"Berry MP","year":"2010","unstructured":"MP Berry, et al., An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466, 973\u2013977 (2010).","journal-title":"Nature"},{"key":"e_1_3_4_65_2","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1038\/msb.2008.55","article-title":"InnateDB: Facilitating systems-level analyses of the mammalian innate immune response","volume":"4","author":"Lynn DJ","year":"2008","unstructured":"DJ Lynn, et al., InnateDB: Facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 4, 218 (2008).","journal-title":"Mol Syst Biol"},{"key":"e_1_3_4_66_2","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1089\/jir.1995.15.517","article-title":"Involvement of two regulatory elements in interferon-gamma-regulated expression of human indoleamine 2,3-dioxygenase gene","volume":"15","author":"Chon SY","year":"1995","unstructured":"SY Chon, HH Hassanain, R Pine, SL Gupta, Involvement of two regulatory elements in interferon-gamma-regulated expression of human indoleamine 2,3-dioxygenase gene. J Interferon Cytokine Res 15, 517\u2013526 (1995).","journal-title":"J Interferon Cytokine Res"},{"key":"e_1_3_4_67_2","doi-asserted-by":"crossref","first-page":"2849","DOI":"10.1073\/pnas.0610944104","article-title":"Distinct modes of action applied by transcription factors STAT1 and IRF1 to initiate transcription of the IFN-gamma-inducible gbp2 gene","volume":"104","author":"Ramsauer K","year":"2007","unstructured":"K Ramsauer, et al., Distinct modes of action applied by transcription factors STAT1 and IRF1 to initiate transcription of the IFN-gamma-inducible gbp2 gene. Proc Natl Acad Sci USA 104, 2849\u20132854 (2007).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_68_2","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1038\/sj.cdd.4401213","article-title":"Involvement of interferon regulatory factor-1 in monocyte CD95 expression and CD95-mediated apoptosis","volume":"10","author":"Conte E","year":"2003","unstructured":"E Conte, et al., Involvement of interferon regulatory factor-1 in monocyte CD95 expression and CD95-mediated apoptosis. Cell Death Differ 10, 615\u2013617 (2003).","journal-title":"Cell Death Differ"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1208972109","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T05:27:37Z","timestamp":1654579657000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1208972109"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,11,14]]},"references-count":73,"journal-issue":{"issue":"50","published-print":{"date-parts":[[2012,12,11]]}},"alternative-id":["10.1073\/pnas.1208972109"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1208972109","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,11,14]]},"assertion":[{"value":"2012-11-14","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}