T-cell differentiation: chromatin remodelling in CD4/CD8 regulation

Single-cell detection of primary transcripts, their genomic loci and nuclear factors by 3D immuno-RNA/DNA FISH in T cells

Over the past decades, it has become increasingly clear that higher order chromatin folding and organization within the nucleus is involved in the regulation of genome activity and serves as an additional epigenetic mechanism that modulates cellular functions and gene expression programs in diverse biological processes. In particular, dynamic allelic interactions and nuclear locations can be of functional importance during the process of lymphoid differentiation and the regulation of immune responses. Analyses of the proximity between chromatin and/or nuclear regions can be performed on populations of cells with high-throughput sequencing approaches such as chromatin conformation capture ("3C"-based) or DNA adenine methyltransferase identification (DamID) methods, or, in individual cells, by the simultaneous visualization of genomic loci, their primary transcripts and nuclear compartments within the 3-dimensional nuclear space using Fluorescence In Situ Hybridization (FISH) and immunostaining. Here, we present a detailed protocol to simultaneously detect nascent RNA transcripts (3D RNA FISH), their genomic loci (3D DNA FISH) and/or their chromosome territories (CT paint DNA FISH) combined with the antibody-based detection of various nuclear factors (immunofluorescence). We delineate the application and effectiveness of this robust and reproducible protocol in several murine T lymphocyte subtypes (from differentiating thymic T cells, to activated splenic and peripheral T cells) as well as other murine cells, including embryonic stem cells, B cells, megakaryocytes and macrophages.

The regulatory network that controls the differentiation of T lymphocytes

There is a vast amount of molecular information regarding the differentiation of T lymphocytes, in particular regarding in vitro experimental treatments that modify their differentiation process. This publicly available information was used to infer the regulatory network that controls the differentiation of T lymphocytes into CD4(+) and CD8(+) cells. Hereby we present a network that consists of 50 nodes and 97 regulatory interactions, representing the main signaling circuits established among molecules and molecular complexes regulating the differentiation of T cells. The network was converted into a continuous dynamical system in the form of a set of coupled ordinary differential equations, and its dynamical behavior was studied. With the aid of numerical methods, nine fixed point attractors were found for the dynamical system. These attractors correspond to the activation patterns observed experimentally for the following cell types: CD4(-)CD8(-), CD4(+)CD8(+), CD4(+) naive, Th1, Th2, Th17, Treg, CD8(+) naive, and CTL. Furthermore, the model is able to describe the differentiation process from the precursor CD4(-)CD8(-) to any of the effector types due to a specific series of extracellular signals.

CD4+ CD8+ double positive (DP) T cells in health and disease

The expression of CD4 and CD8alphabeta co-receptors on mature T cells is generally considered to be mutually exclusive and reflects subset-related, specific functions (helper vs. cytolytic) and differences in major histocompatibility complex-restriction for antigen recognition. However, double positive (DP) T cells expressing both CD4 and CD8 have been described in several pathological conditions as well as in normal individuals. DP T cells represent a heterogeneous population. Strong evidence indicates that in vivo terminally differentiated effector CD4 may acquire the alpha-chain of CD8. Reciprocally, in vitro activation of CD8+ T cells results in the expression of low levels of CD4 that may mediate HIV entry and responses to chemotactic cytokines. Particularly intriguing, a subset of DP T cells expressing high levels of both CD4 and CD8alphabeta heterodimer (CD4(hi)CD8(hi)), has been identified in autoimmune and chronic inflammatory disorders. While no definitive proof exists, it could be speculated that CD4(hi)CD8(hi) T cells may be endowed with auto-reactivity due to faulty thymic selection.

Immunity and the Animation of the Genome

Expression of genes in the right place at the right time is fundamental to all of life. The ontogeny of effector and memory T cells is a robust example of this important principle. Although lymphocytes represent a late addition in animal evolution, they are serving as an exceptional model system to unlock the mysteries surrounding the way in which the genome is animated. It will be speculated here that further insight into fundamental principles of genome function may arise from study of immunity. Likewise, such information may be key to understanding and altering immunobiology.