Characterization of CD8+ T Cell Differentiation following SIVΔnef Vaccination by Transcription Factor Expression Profiling

Authors

James M. Billingsley, Emory University
Premeela A. Rajakumar, Emory University
Michelle A. Connole, Harvard Medical School
Nadine C. Salisch, Emory University
Sama Adnan, Emory University
Yury V. Kuzmichev, Harvard Medical School
Henoch S. Hong, Harvard Medical School
R. Keith Reeves, Harvard Medical School
Hyung-joo Kang, University of Massachusetts Medical Center
Wenjun Li, University of Massachusetts Medical Center
Qingsheng Li, University of Nebraska-LincolnFollow
Ashley T. Haase, University of MinnesotaFollow
R. Paul Johnson, Emory UniversityFollow

Document Type

Article

Date of this Version

2015

Citation

Billingsley JM, Rajakumar PA, Connole MA, Salisch NC, Adnan S, Kuzmichev YV, et al. (2015) Characterization of CD8+ T Cell Differentiation following SIVΔnef Vaccination by Transcription Factor Expression Profiling. PLoS Pathog 11(3): e1004740. doi:10.1371/journal.ppat.1004740

Comments

© 2015 Billingsley et al. This is an open access article distributed under the terms of the Creative Commons Attribution License.

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.