Reevesdunlap5513

Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) is an invaluable method to profile of enrichment of histone modifications and transcription factor binding sites across the genome. However, standard ChIP-seq protocols require large numbers of cells (>107) as starting material, which are often impossible to obtain for rare immune populations. Here we describe a streamlined ChIP protocol optimised for small cell numbers in conjunction with transposon-tagging mediated sequencing library preparation (ChIPmentation) which allows the analysis of samples of as low as 105 cells.Flow cytometric evaluation of phosphorylation status of signal transduction molecules is a useful method to study T-cell signaling pathways. As mutations occurring in TCR complex molecules, common gamma chain family's cytokines, their receptors or molecules involved in these pathways can lead to severe immune system defects, the study of T-cell signal transduction can be applied to both basic and clinical/translational research areas. In the present chapter, we show two different protocols for the study of T- cell response to an antigen-like stimulus and to IL-2.Antibody responses deeply rely on the interaction of antigen-primed B cells and CD4 helper T cells in the context of germinal center reactions, through signals provided by costimulatory molecules and cytokines. B-cell proliferation and differentiation in antibody-secreting plasma cells are processes that critically depend on the helper function of a specific CD4 T-cell subset, known as follicular helper T cells (Tfh). Here, we describe a method that mimics in vitro the cross talk between Tfh and B cells occurring in the germinal center. The procedure is based on setting up a coculture system with B cells and Tfh isolated from blood of healthy donors, or tonsils removed upon surgical intervention, in order to recapitulate in vitro the Tfh-dependent mechanisms leading to B cells' activation, proliferation, and differentiation.Human T cells represent a heterogeneous population, including cells with different phenotypical and function properties. Despite, in the last years, several technologies were developed to investigate phenotypical properties of T cells at single cell level, in vitro T cell clone 's culture remains the only way to perform functional study on T cells at single cell levels. Here, we describe the method to obtain human T cell clones by limiting dilution in the presence of feeder cells and to maintain them in culture for further investigations.Peptide-major histocompatibility complex class II (pMHCII) multimers have emerged as a convenient and powerful tool for characterization of CD4 T cell immune responses in a large variety of human diseases. Peptide-MHCII multimers can rapidly identify peptide antigens recognized by CD4 T cells via high-throughput peptide screening procedures. The specificity and phenotype of antigen-specific CD4 T cells can be effectively visualized by pMHCII multimers from unmanipulated immune cell populations. Functional attributes of antigen-specific CD4 T cells can also be defined with the multimer technology in combination with immune functional assays such as intracellular cytokine staining (ICS).The detection and functional characterization of antigen-reactive T helper (Th) cells has been challenging due to their low frequency and functional heterogeneity. Antigen-reactive T cell enrichment (ARTE) allows the in-depth characterization of antigen-specific Th lymphocytes as a prerequisite for better understanding the role of adaptive immune responses in health and disease. ARTE is based on detection of the activation markers CD154 (CD40L) (expressed on all conventional Th cell subsets, Tcons) and CD137 (4-1BB) (expressed on regulatory T cells, Tregs), which are upregulated on the surface of CD4+ T cells upon short-term (7 h) in vitro stimulation with antigens in the presence of antigen-presenting cells (APCs). this website To substantially increase the sensitivity for the detection of antigen-specific Th cells, ARTE combines magnetic pre-enrichment of rare antigen-reactive T cells with multiparameter flow cytometry. Using CD154 and CD137 in combination allows the parallel detection of reactive Tcons and Tregs, after stimulation with the antigen. Thus, the ARTE technology now enables to characterize antigen-specific T cells with increased sensitivity of detection allowing even the investigation of antigen-specific Th cells in the naive T cell repertoire and regardless of prior knowledge of MHC alleles or antigenic epitopes.A critical property of T cells when activated by their cognate antigen-MHC complex is the initiation of cell cycle activity and clonal expansion. In this chapter, we describe how the proliferation of T cells can be assessed on the single cell level by flow cytometry and how this can be used to identify and potentially isolate antigen-reactive T cells.The Luminex XMAP technology permits the simultaneous evaluation of numerous cytokines in several types of biological fluids (plasma, serum, liquor, follicular fluids, etc.) and in cell supernatants. Thus, multiplexing allows to achieve a time/cost economy and ensures that all the measurements are performed in the same conditions. Simultaneous measurement of cytokines with a multiplex bead-based assay has some similarities with ELISA, in particular the use of anti-cytokine antibodies, but shows an important difference, the use of magnetic fluorescent beads coupled to anti-cytokine monoclonal antibodies. The magnetic microspheres (dyed internally with two florescent dyes) coupled with anti-cytokine monoclonal antibodies are incubated with samples and standards; after washing, the samples/standards are incubated with biotinylated anti-cytokine monoclonal antibodies; and finally, after other washings, with streptavidin-phycoerythrin solution. Luminex instrument identifies the different cytokines present in each well and converts the mean fluorescence intensity (MFI) of each measured cytokine in pg/ml, thanks to the software and the standard curves. This technique is applicable in basic and clinical research.