The Chromatin and Epigenetics fields have experienced a spectacular development in the last few years. Key breakthroughs include the identification of a code of histone modifications associated with specific functions, the finding of mechanistic links between DNA methylation and histone modifications or the recognition that epigenetic modifications and chromatin organization not only define cell identity but also constitutes a dynamic readout of environment. But most importantly, the identification of alterations in chromatin structure and epigenetic regulation in diseases including cancer, autoimmune disease, and a variety of syndromes, have added a clinical dimension to studies in chromatin and epigenetics, since these alterations are potentially reversible.

The study of lymphocyte differentiation and activation allows us to understand not only mechanisms of epigenetic regulation and chromatin organization but also how the abnormal control of these pathways can lead to abnormal behaviour in haematopoietic malignancies or other diseases such as autoimmune disorders. Appropriate cell fate decissions and maintenance of homeostasis are key in maintaining the normal behaviour of haematopoietic and immune system. Lymphocyte differentiation and activation involve many different transcription factors, including Runx1, PAX5, GATA3, all Ikaros and Notch family members or polycomb group proteins, that associate with the epigenetic machinery. In general, subsequent and specific expression of these transcription factors is associated with differentiation. Additionally, microRNAs (miRNAs), an important group of transcriptional regulators that affect the translation and/or the stability of protein-coding transcripts, have also been involved in lymphocyte differentiation. These processes are orchestrated in response to discrete intracellular signaling pathways, including phosphorylation cascades that culminate in the activation of mitogen-activated protein kinases (MAPKs). Connections between signaling cascades and epigenetic modifications have particular relevance for cells that participate in immune and inflammatory response.

In this context, there are fundamental questions that remain to be aswered including the mechanisms of epigenetic regulation of transcription factors and miRNAs and their functional consequences in lymphocyte differentation. In addition, the mechanisms by which signaling pathways result in epigenetic regulation are unknown. The consequences of misregulation of these processes have been proposed to participate in haematopoietic disorders, including leukemias, lymphomas on one hand, or autoimmune disease, on the other; however the detailed mechanisms are also unknown. Our group is focused on the epigenetic alterations the haematopoietic system and their connections with upstream signaling pathways.

We are currently interested in investigating the implication of the epigenetic inactivation of transcriptional factors involved in lymphocyte differentiation in the development of haematopoietic malignancies. For instance, when analysing at all the Ikaros family members we have found that some are specifically methylated in certain lymphomas and leukemias. Methylation of Ikaros and Aiolos may contribute to an impairment of differentiation.

Recently, miRNAs have also been implicated in many differentiation processes. In fact, there are specific sets of miRNAs expressed per cell in different stages of lymphocyte differentiation. We are also interested in investigating the epigenetic mechanisms that control miRNA expression throughout lymphocyte differentiation and their functional consequences.

-Epigenetic Mechanisms involved in T cell Activation processes. Exposure of naive lymphocytes to antigens results in further differentiation, in a process known as activation. Proinflammatory cytokines and microbial products stimulate transcription of several genes involved in the inflammatory and immune response through the coordinate induction of multiple signaling pathways, including three major mitogen-activated protein kinase (MAPK) pathways –Erks, p38 and c-Jun kinases. One of the most studied MAPKs, p38, has been directly involved in the expression of several immune response genes through chromatin signaling. T cells activate p38 MAPK via two distinct pathways, the classical MAPK cascade and a newly described alternative pathway, which is independent of MAPKK-mediated phosphorylation. Recently, Gadd45a has been found to inhibit this T cell specific p38 activity, however the downstream events are still unclear. Interestingly, T cell activation has been demonstrated to be associated with selective demethylation of the regulatory sequences of key genes, such as interleukins, interferon etc. On the other hand, in a different context, gadd45a has been recently reported to promote active demethylation.
In order to investigate the connections between the p38 MAPK pathway and the epigenetic regulation of proinflammatory genes, we are studying the epigenetic consequences of genetic or pharmacological inhibition of p38, and subsequent blockage of lymphocyte activation, in the promoter of inflammatory genes in T cells.

-Epigenetic Deregulation in Autoimmune Disease. Epigenetic alterations have long been recognized to occur in autoimmune disease. At a macroscopic level, the epigenetic contribution to the development of autoimmunity is also evidenced in monozygotic twins that are discordant for the disease. An archetypical example of autoimmune disease is provided by systemic lupus erythematosus (SLE), a disease in which both increased rate of apoptosis of T cells, with subsequent release of nuclear components, and exacerbated activation of T and B-cells occur. In both processes, epigenetic alterations have been proposed to be implicated. Remarkably, both global and gene-specific promoter demethylation occur in T cells isolated from both a SLE mouse model and SLE patients. In addition, several histone deacetylase (HDAC) and DNA methyltransferase inhibitors affect the epigenetic status of inflammatory genes in T cells isolated from SLE patients and have effects in the phenotype of both SLE patients and murine models. Interestingly, Gadd45a knockout mice, which show hyperactivation of T cells, develop a SLE-like phenotype.
One of the aims of our group will focus on the study of the epigenetic mechanisms implicated in autoimmune disease, as a strategy to better understand epigenetic regulation of lymphocyte activation. Our research plan is focused in obtaining detailed maps of epigenetic alterations in T and B cells from both mouse models for SLE and human samples. This characterization will be followed by a characterization of the elements of the chromatin machinery involved in the establishment of the proper and aberrant proifile of epigenetic marks and a study of potential reversion of altered patterns. Finally, a study of the implication of upstream signalling cascades (p38 MAP and PI3K) in the generation of aberrant chromatin patterns will be studied.