Clonal Selection in CD4 T cells: the role of TCR specificity and avidity

The ability to distinguish self from nonself is a fundamental property of the innate and adaptive immune system. For the somatically generated repertoire of T cell and B cell antigen receptors (TCR and BCR, respectively), self–nonself discrimination is primarily achieved through clonal deletion of lymphocytes expressing strongly auto-reactive receptors. Removal of such receptors from the TCR and BCR repertoires causes irreversible self-tolerance. For a T cell, this is a precarious life. During development in the thymus it must adopt a certain degree of self-reactivity in order to pass selection criteria, yet this must fall below a threshold, which would flag it to be negatively selected. This rigorous purging sees only approximately 3-5% of candidate thymocytes making it through the process. Once in the periphery, the quality of TCR signaling continues to be important and is heavily censored by extrinsic factors, which actively shape and condition both the pre-immune and antigen-responding repertoire. Although it is very clear that the signaling capacity of the TCR, whether this be towards self or nonself, is a key determinant in defining the trajectory of a T cell, the degree to which it governs these fate decisions remains ill defined. This thesis examines the relationship that exists between the T cell and its TCR throughout the life of a T cell

Cohesin-dependence of neuronal gene expression relates to chromatin loop length

Cohesin and CTCF are major drivers of 3D genome organization, but their role in neurons is still emerging. Here, we show a prominent role for cohesin in the expression of genes that facilitate neuronal maturation and homeostasis. Unexpectedly, we observed two major classes of activity-regulated genes with distinct reliance on cohesin in mouse primary cortical neurons. Immediate early genes (IEGs) remained fully inducible by KCl and BDNF, and short-range enhancer-promoter contacts at the IEGs Fos formed robustly in the absence of cohesin. In contrast, cohesin was required for full expression of a subset of secondary response genes characterized by long-range chromatin contacts. Cohesin-dependence of constitutive neuronal genes with key functions in synaptic transmission and neurotransmitter signaling also scaled with chromatin loop length. Our data demonstrate that key genes required for the maturation and activation of primary cortical neurons depend on cohesin for their full expression, and that the degree to which these genes rely on cohesin scales with the genomic distance traversed by their chromatin contacts. Editor'

Inhibition of alpha nascent polypeptide associated complex protein may induce proliferation, differentiation and enhance the cytotoxic activity of human CD8+ T cells

The molecular mechanisms that control CD8+ T cell proliferation and differentiations are poorly understood. Consequently, better understanding of the molecular pathways that regulate these processes may have an impact on the numbers and efficiency of antigen-specific cells that can be generated for cellular immunotherapy applications. Using differential display, we previously determined that alpha nascent polypeptide associated complex (α NAC) was identified as a potential target as its protein expression was found to be down-regulated as differentiation progressed in cultured human CD8+ T cells. Here anti-sense technology was used to further investigate the role which α NAC may play in proliferation and differentiation. Human purified CD8+ T cells were cultured in the presence of sense, non-sense and anti-sense oligonucleotides against the mRNA of α NAC. We reported that in the presence of anti-sense oligonucleotides expanded CD8+ T cells exhibited higher levels of differentiation and activation markers and also increased proliferation response compared to cells cultured with sense-oligonucleotides. Furthermore, the functional cytotoxicity of CD8+ T cells cultured with anti-sense was increased to 66% (±4.7%) compared to 42% (±3.2%) in cells expanded in the presence of oligonucleotides controls. Taken together, our results demonstrated that inhibition of α NAC protein induced not only cell proliferation but also differentiation and cytotoxic activity of CD8+ T cells

Sustained calcium signalling and caspase-3 activation involve NMDA receptors in thymocytes in contact with dendritic cells

L-glutamate, the major excitatory neurotransmitter, also has a role in non-neuronal tissues and modulates immune responses. Whether NMDA receptor (NMDAR) signalling is involved in T-cell development is unknown. In this study, we show that mouse thymocytes expressed an array of glutamate receptors, including NMDARs subunits. Sustained calcium (Ca2+) signals and caspase-3 activation in thymocytes were induced by interaction with antigen-pulsed dendritic cells (DCs) and were inhibited by NMDAR antagonists MK801 and memantine. NMDARs were transiently activated, triggered the sustained Ca2+ signal and were corecruited with the PDZ-domain adaptor postsynaptic density (PSD)-95 to thymocyte-DC contact zones. Although T-cell receptor (TCR) activation was sufficient for relocalization of NMDAR and PSD-95 at the contact zone, NMDAR could be activated only in a synaptic context. In these T-DC contacts, thymocyte activation occurred in the absence of exogenous glutamate, indicating that DCs could be a physiological source of glutamate. DCs expressed glutamate, glutamate-specific vesicular glutamate transporters and were capable of fast glutamate release through a Ca2+-dependent mechanism. We suggest that glutamate released by DCs could elicit focal responses through NMDAR-signalling in T cells undergoing apoptosis. Thus, synapses between T and DCs could provide a functional platform for coupling TCR activation and NMDAR signalling, which might reflect on T-cell development and modulation of the immune response

Genome organization and DNA accessibility control antigenic variation in trypanosomes.

Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host1. Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by three-dimensional genome architecture and local DNA accessibility2,3. Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotype-specific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using long-read sequencing technology and conserved features of chromosome folding4. Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses—Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing—that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation