8. T Cell Epitope-Mapping by Cytokine Gene Expression Assay
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The following method describes the identification of candidate immunogenic peptides through their ability to recall an immune
T-cell activation from peripheral blood mononuclear cells (PBMCs) of individuals with defined HLA–peptide restrictions that
have been previously exposed to the antigen. Isolated PBMCs are plated out at a concentration of 1×106 cells/ml in a 200 μl medium and incubated overnight to reduce cytokine gene expression due to cell manipulation. After starving,
cells are either directly stimulated with individual peptides or not stimulated and incubated from 3 to 12 h according to
experimental conditions. Quantitative real-time PCR (qrt-PCR) is performed on reverse-transcribed complementary DNA (cDNA)
from total RNA that is isolated from peptide-cultured PBMCs. To perform high quality qrt-PCR, primers and probes are designed
to span exon–intron junctions in order to prevent amplification of genomic DNA and to produce amplicons <150 base pairs (bp).
Real-time monitoring of fluorescent emission from the cleavage of sequence specific probe by the nuclease activity of Taq polymerase (TaqMan method) defines threshold cycles during exponential phases of amplification. Standard curves of copy numbers
of the gene of interest are normalized using as reference copy numbers of control genes.
Affiliation(s): (3) Department of Urology, University Hospital of Zurich, Zurich, Switzerland
(4) Institute of Surgical Research and Hospital Management, University Hospital Basel, Basel, Switzerland
(4) Institute of Surgical Research and Hospital Management, University Hospital Basel, Basel, Switzerland
Book Title: T Cell Protocols: Second Edition
Series: Methods in Molecular Biology | Volume: 514 | Pub. Date: Jul-01-2008 | Page Range: 107-118 | DOI: 10.1007/978-1-60327-527-9_8
Subject: Immunology
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