Transcriptional control of human T lymphocyte pathogenic potential in autoimmunity

T helper lymphocytes are essential for productive immune responses against invading pathogens, but autoreactive T cells responding against self-antigens are also major determinants of immune-mediated disorders. Multiple sclerosis (MS) is a chronic inflammatory disease with an underlying autoimmune etiology, likely to be initiated by T lymphocytes recognizing myelin self-antigens. Circulating myelin-autoreactive T lymphocytes are also found in healthy individuals, with a frequency similar to that of MS patients, indicating that the mere presence of autoreactive cells is insufficient to explain autoimmune responses, and that mechanisms that regulate the threshold, magnitude and the inflammatory potential of T cell responses are instead crucial for autoimmunity to occur, and may therefore represent relevant therapeutic targets. Both genetic and environmental factors are known to influence the onset and course of autoimmune diseases, and epigenetic mechanisms of transcriptional regulation appear particularly suited to translate environmental cues into stable, yet reversible modifications in gene expression. Indeed, it has become increasingly clear that epigenetic modifications such as methylation of the genomic DNA can be dynamic and able to adapt to the changing environment, with an important impact on a number of diseases, including autoimmunity. However, a number of outstanding questions regarding the role of these modifications in affecting genomic readouts in general, and transcriptional responses of T lymphocytes in particular still remain unanswered. With the overall goal of identifying molecular mechanisms that contribute to the control of T cell responses in autoimmunity in humans, we propose the following:•Aim 1: To comprehensively investigate the role of DNA modifications in human T cell responses and specifically in regulating the balance between pro- and anti-inflammatory phenotypes or states. This will be performed by analyzing the role of DNA methylation and hydroxymethylation in human T cells in response to a variety of antigens. The impact of the epigenome on gene expression will be also investigated, as well as the relative role of enzymatic activity-dependent and independent functions of the DNA modifying enzymes, in order to thoroughly define the link between epigenetic modifications, gene expression and T cell phenotype.DNA methylation is deeply interconnected with transcription factor (TF) binding, in that methylation can recruit or repel specific binders or readers, and the presence or absence of a modified cytosine within the binding site for a TF can alter TF-binding specificity. Conversely, TF binding can lead to, or prevent epigenetic modifications in the genome, ultimately altering the gene expression program of a cell. With the general goal of becoming able to modulate specific pathogenic properties in T lymphocytes and eventually influence the outcome of autoimmune pathology we propose the following:•Aim 2: To identify TF determinants able to reprogram pathogenic, highly pro-inflammatory T cells in patients with MS and reduce their pathogenicity. This will be performed combining cutting-edge cellular immunology techniques with the functional and mechanistic analyses of such factors, including understanding the role of DNA methylation in altering TF expression and/ or binding. We will also assess histone modifications at sites of TF binding to understand the downstream effect of TF binding on chromatin remodeling and gene expression.