title: Characterization of CD8+ T cell differentiation following SIVΔnef vaccination by transcription factor expression profiling.
abstract: The onset of protective immunity against pathogenic SIV challenge in SIVΔnef-vaccinated macaques is delayed for 15-20 weeks, a process that is related to qualitative changes in CD8+ T cell responses induced by SIVΔnef. As a novel approach to characterize cell differentiation following vaccination, we used multi-target qPCR to measure transcription factor expression in naïve and memory subsets of CD8++ T cells, and in SIV-specific CD8+ T cells obtained from SIVΔnef-vaccinated or wild type SIVmac239-infected macaques. Unsupervised clustering of expression profiles organized naïve and memory CD8+ T cells into groups concordant with cell surface phenotype. Transcription factor expression patterns in SIV-specific CD8+ T cells in SIVΔnef-vaccinated animals were distinct from those observed in purified CD8+ T cell subsets obtained from naïve animals, and were intermediate to expression profiles of purified central memory and effector memory T cells. Expression of transcription factors elicited by SIVΔnef vaccination also varied over time: cells obtained at later time points, temporally associated with greater protection, appeared more central-memory like than cells obtained at earlier time points, which appeared more effector memory-like. Expression of transcription factors associated with effector differentiation, such as ID2 and RUNX3, were decreased over time, while expression of transcription factors associated with quiescence or memory differentiation, such as TCF7, BCOR and EOMES, increased. CD8+ T cells specific for a more conserved epitope expressed higher levels of TBX21 and BATF, and appeared more effector-like than cells specific for an escaped epitope, consistent with continued activation by replicating vaccine virus. These data suggest transcription factor expression profiling is a novel method that can provide additional data complementary to the analysis of memory cell differentiation based on classical phenotypic markers. Additionally, these data support the hypothesis that ongoing stimulation by SIVΔnef promotes a distinct protective balance of CD8+ T cell differentiation and activation states.
authors.affiliation: Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America; Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America.
authors.forename: James M
authors.initials: JM
authors.lastname: Billingsley
authors.affiliation: Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America; Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America.
authors.forename: Premeela A
authors.initials: PA
authors.lastname: Rajakumar
authors.affiliation: Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America.
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Connole
authors.affiliation: Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America; Crucell Holland BV, Leiden, The Netherlands.
authors.forename: Nadine C
authors.initials: NC
authors.lastname: Salisch
authors.affiliation: Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America; Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America.
authors.forename: Sama
authors.initials: S
authors.lastname: Adnan
authors.affiliation: Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America.
authors.forename: Yury V
authors.initials: YV
authors.lastname: Kuzmichev
authors.affiliation: Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America.
authors.forename: Henoch S
authors.initials: HS
authors.lastname: Hong
authors.affiliation: Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America.
authors.forename: R Keith
authors.initials: RK
authors.lastname: Reeves
authors.affiliation: Division of Preventive and Behavioral Medicine, University of Massachusetts Medical Center, Worcester, Massachusetts, United States of America.
authors.forename: Hyung-joo
authors.initials: HJ
authors.lastname: Kang
authors.affiliation: Division of Preventive and Behavioral Medicine, University of Massachusetts Medical Center, Worcester, Massachusetts, United States of America.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Li
authors.affiliation: Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.
authors.forename: Qingsheng
authors.initials: Q
authors.lastname: Li
authors.affiliation: University of Minnesota, Microbiology Department, Minneapolis, Minnesota, United States of America.
authors.forename: Ashley T
authors.initials: AT
authors.lastname: Haase
authors.affiliation: Division of Immunology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America; Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America; Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America.
authors.forename: R Paul
authors.initials: RP
authors.lastname: Johnson
mesh_terms: D000818:Animals; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology* / Q000473:pathology; D002454:Cell Differentiation / Q000276:immunology; D005260:Female; D020869:Gene Expression Profiling; D007156:Immunologic Memory; D008253:Macaca mulatta; D018449:SAIDS Vaccines / Q000235:genetics / Q000276:immunology*; D015302:Simian Immunodeficiency Virus / Q000235:genetics / Q000276:immunology*; D014157:Transcription Factors / Q000235:genetics / Q000276:immunology*; D054334:Viral Regulatory and Accessory Proteins
chemical_list: C429284:NEF protein, SIV; D018449:SAIDS Vaccines; D014157:Transcription Factors; D054334:Viral Regulatory and Accessory Proteins