title: Pooled-Peptide Epitope Mapping Strategies Are Efficient and Highly Sensitive: An Evaluation of Methods for Identifying Human T Cell Epitope Specificities in Large-Scale HIV Vaccine Efficacy Trials.
abstract: The interferon gamma, enzyme-linked immunospot (IFN-γ ELISpot) assay is widely used to identify viral antigen-specific T cells is frequently employed to quantify T cell responses in HIV vaccine studies. It can be used to define T cell epitope specificities using panels of peptide antigens, but with sample and cost constraints there is a critical need to improve the efficiency of epitope mapping for large and variable pathogens. We evaluated two epitope mapping strategies, based on group testing, for their ability to identify vaccine-induced T-cells from participants in the Step HIV-1 vaccine efficacy trial, and compared the findings to an approach of assaying each peptide individually. The group testing strategies reduced the number of assays required by >7-fold without significantly altering the accuracy of T-cell breadth estimates. Assays of small pools containing 7-30 peptides were highly sensitive and effective at detecting single positive peptides as well as summating responses to multiple peptides. Also, assays with a single 15-mer peptide, containing an identified epitope, did not always elicit a response providing validation that 15-mer peptides are not optimal antigens for detecting CD8+ T cells. Our findings further validate pooling-based epitope mapping strategies, which are critical for characterizing vaccine-induced T-cell responses and more broadly for informing iterative vaccine design. We also show ways to improve their application with computational peptide:MHC binding predictors that can accurately identify the optimal epitope within a 15-mer peptide and within a pool of 15-mer peptides.
authors: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.
authors: Andrew
authors: A
authors: Fiore-Gartland
authors: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.
authors: Bryce A
authors: BA
authors: Manso
authors: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.
authors: David P
authors: DP
authors: Friedrich
authors: Biostatistics Research Branch, National Institute of Allergy and Infectious Disease, Rockville, Maryland, 20852, United States of America.
authors: Erin E
authors: EE
authors: Gabriel
authors: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.
authors: Greg
authors: G
authors: Finak
authors: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.
authors: Zoe
authors: Z
authors: Moodie
authors: Shraga Segal Department of Microbiology, Immunology and Genetics, Ben Gurion Institute of the Negev, Beer-Sheva, 84105, Israel.
authors: Tomer
authors: T
authors: Hertz
authors: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.
authors: Stephen C
authors: SC
authors: De Rosa
authors: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.
authors: Nicole
authors: N
authors: Frahm
authors: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.
authors: Peter B
authors: PB
authors: Gilbert
authors: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.
authors: M Juliana
authors: MJ
authors: McElrath
mesh_terms: D016915:AIDS Vaccines / Q000276:immunology* / Q000627:therapeutic use; D000293:Adolescent; D000328:Adult; D018414:CD8-Positive T-Lymphocytes / Q000166:cytology*; D002986:Clinical Trials as Topic; D015331:Cohort Studies; D004311:Double-Blind Method; D058501:Enzyme-Linked Immunospot Assay; D018604:Epitope Mapping / Q000379:methods*; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry*; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D010455:Peptides / Q000737:chemistry*; D015203:Reproducibility of Results; D012107:Research Design; D012680:Sensitivity and Specificity; D055815:Young Adult
chemical_list: D016915:AIDS Vaccines; D018984:Epitopes, T-Lymphocyte; D010455:Peptides